Every 2-3 years or so I replace my blue body geometry insoles in my specialized shoes. Been doing this for over 10 yrs now. They have good arch support etc. I replace them as a preventative measure as I can feel the support lacking over time. Well after a week of indoor riding only with just Petit endurance ride, I started developing knee pain in both knees. It shows up in bed mostly afterwards. Feels near the quadricep/ kneecap tendon/ under kneecap. How does one little change I’ve always been doing screw me up so badly? My foot really feels comfortable inside and I can tell the added stability. I still have my old insoles. Should I just switch back and never do this again ?
Did you just start indoor training again or had you been doing it for a bit and then made the switch?
Your feet may have changed to the worn out insole, lower arches, etc and now it doesn’t feel correct to them.
May need a different insole or your legs may just get used to it.
I’ve been indoor riding consistently all year. I only change equipment during the off season. Maybe I should just do less intense and hopefully over a month or so get used to it or just go back to old ones and see if it eliminates the issue? It only seems to affect me a few hours after and not during
Give it a few days. The new insole likely just changed your alignment a mm or so, your body will get used to it. If its real pain, then take them out, if its just a little soreness, give it time
I agree with the “give it time” although since you have your old ones you could easily switch back and forth for a ride and see if that really is the difference. Don’t mess with anything else though while you figure it out.
After years of dealing with knee pain plus all of the stuff about how your power changes as you move your saddle up and down, I have developed a fixation on my saddle height. I feel like I’m not getting enough power → i put my seat up a couple of mm → i feel fast! → i get knee/hip/low back pain or saddle sores → i move it back down → i feel fast!! It took me until this summer (i’ve been in this cycle for almost 10 years) to realize that I have a tendency to think that my saddle is too low whenever my legs are actually just tired. So I don’t need to move my seat - I just need to take a rest day and leave my saddle where it is. And then I don’t get any pain from messing with it.
So anyways, be careful of these associations you create in your mind.
It may not be your issue, but having just bought some of these, there seem to be 2 generations in the market at the moment.
Is it possible you’ve swapped generations causing your issue?
I was going to mention this… I was looking at these earlier this year and I thought I came across some reviews saying that they updated their insoles!
I’ll have to look at the box. But they look exactly the same as before. On the website of LBS it just says SL. - Gen2 Insoles function the same as Gen1 but have a broader toe profile to match the new Ares 2 shoe. They feature a moulded cut line to suit any other shoe.
so I don’t think gen 2 would even fit my shoes.
they look like gen 1 where I got them. But will compare the front shape to make sure.
Does your body want to change the position and with that put less strain on the fatigued muscles?
I myself can get additional minutes of power with positional changes. It‘s not much but may help to finish some intervals.
Well I checked and they are indeed SL gen 1 footbed. Comparing the two the newer ones just feel stiffer. That’s the only difference. Don’t know how that can cause such an issue. Will try going slowly over next few weeks to see if it improves. Was already taking it easy so petit -1 will have to do. Looking at loosing lots of fitness I guess. Hope the damage wasn’t already done and will be hard to get back in. Got runners knee 13 years ago and it was hard to get back. This feels similar.
This is usually on an outdoor bike where I’m moving around a decent amount anyways
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Similar be different, i just added a couple washers to increase my Q factor. First 3 ride both knees a little soreness. After that i was good to go. Tiny changes add up when your turning the pedals 10s of thousands times….takes some time to adjust.
I have abused the higher saddle-height gives more power a few times on long (HC) full-gas hillclimb segment attempts, though after struggling with some knee issues this season I may not do that again. 
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Well after giving it a try for a week going slowly soreness remained. I switched back to my old soles but it’s like the damage was done. I can do 45min easy endurance ride but the moment I try a 1h endurance ride I get soreness top of kneecap in just my left knee. It’s probably petellofemoral syndrome.
I had something similar 13 years ago after doing a. 170km ride. It taught me to foam rolll, stretch and strengthen muscles off the bike. Been doing it religiously for all this time. Don’t know what I’m going to do now.
This generalized dull soreness is only felt the next day. Don’t feel any issues during the workout.
Been meaning to reply to this for a while. I’ve experienced something akin to your problem (specifics differ), starting in August, but I’m well on track to fully recovering from it now so I offer hope…. 
Mid-August I replaced my cycling shoes with an identical (but new!) pair, transferred my custom insoles and varus wedges from the old shoes, and diligently set up the cleats “identically”. Two weeks of riding later, with big miles, and I had significant lateral left side knee pain off the bike (fine while on it!) - had never had a problem with this knee before in 20 yrs of cycling.
Took a while to figure out, but it seems that a plastic spacer sitting between the (MTB-style) cleat and the sole of the shoe had collapsed somewhat causing the cleat to become tilted ever so slightly from the horizontal L-R plane. Because this tilting had occurred slowly over 12 months, my body had adapted to this incremental change without ill effect. The problem was that in my new shoes the new cleat was perfectly horizontal causing extra pressure on the outside of my foot which then transferred to the outside of the knee, and my body couldn’t adapt to this instant change of position.
Like you found, switching back to the OG setup (shoes) didn’t cure me - the damage was already done…
What I did: the most important things were probably regular use of an ice-pack + time for my body to adjust.
I took 10 days off initially, applying an ice-pack to the knee several times/day to reduce inflammation, plus took regular anti-inflammatories. I wanted to retain fitness for an October cycling trip, so when I restarted cycling I cut my volume right down and just did key workouts on the trainer. I applied the ice-pack after every ride, before bed, and also in between whenever practical. The ice-pack was the wonder treatment vs the rest and the anti-inflammatories. Previously I’ve been skeptical of ice but it was absolutely key - after application the soreness just went away for quite some time.
I also made some minor shoe/pedal adjustments, to try to get the foot & knee to feel as stable as possible: I increased the q-factor slightly with a pedal washer, and I increased the instep support within my heat-reshapable custom insoles. But the key things seemed to be ice + time.
I went on my October trip, which I’d initially thought I’d have to cancel, and managed to cycle every day without my knee worsening at all. Super happy with that. I took portable ice packs with me which I applied after every ride, along with anti inflammatories every day and night.
4 1/2 months after this all began, and the knee soreness and the foot stability are still not 100%, but they feel more normal every week that passes, and I’m only occasionally applying the ice now. I’m off on another cycling trip soon, and will take portable ice packs again to help with cycling every day. I hope by the spring - or at latest the summer - the knee and foot stability will be totally back to normal, with my body having fully adapted to the ever-so-slightly changed cleat angle…
It seems a bit crazy that such a minor initial cleat difference could lead to such long-lasting problems but there you go… 
I’ve learned one lesson, and that is to go back to simultaneously running (at least) two pairs of cycling shoes like I used to do. With two or more pairs in active use, there are inevitably always very slight differences in setup between them (cleats, insoles etc), which probably helps prevent the body from becoming quite so sensitive to inadvertent future changes. Plus, you’ve always one good pair to act as a reference when setting up a new one.
Hopefully, with time, your problem will go away as mine seems to be. Hang in there, and get busy with the ice 