So I got a week into my new ftp builder training plan and came down with flu. This has meant missing 2 weeks of the base phase (2 out of 4). Next week is an easy/ recovery week, before the build phase. Should I just start a new training plan or see the plan through?
First, hope you feel better soon! Its that time of the season, so take care of yourself.
Is your training plan set with a goal, ie improving FTP, general fitness, or event based, ie upcoming race? I would probably just reset and start the plan again. Better to start out rested and recovered as the training can pick up and you don’t want to dig yourself into a hole and get sick again.
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If you need the base then start the same plan from the begining. Don’t continue.
If you had a good base then I would proceed with the plan the way it is. TR will figure it out. The rest / recover week will do you good after being sick.
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Normally, if you were doing a program that is not adaptive, I would just start over. Are you training for a specific event or just general fitness? If you don’t have a particular event to train for, I would say just start over. You can put an annotation in TrainingPeaks that you were sick, but I am not sure the adaptive training feature really does anything with that. It would be cool if it did.
With a shorter open ended plan like “raise ftp” I would likely make sure I was back 100% from illness and start the plan then.
I had an illness blow up a raise ftp plan I was going to sneak in before my big season plan. It happens.
Are the adaptive plans not adaptive enough to properly adjust for missing two weeks? How much time or how many workouts can be missed and still have it properly adjust? I’ve done a few plans but never missed significant periods or deviated much from the plan.
Hey @Stressed85, welcome to the forum! 
I agree with the others in that this depends on if you’re using a goal-based or event-based plan.
With event-based plans, we can’t change the end data. That’s determined by your race, so we’ll fill the time in between now and then with the best training we can.
With goal-based plans, however, the end date isn’t necessarily important, so if you want to complete all of the training, feel free to delete your current plan and add in a new one once you’re ready to start training.
If this were to happen, say, halfway through your plan, though, I obviously wouldn’t start over then. 
I can understand your desire to start off on the right foot and get all of your base training in, so either direction will work well enough.
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Thanks I’ll stick with it as the up and coming recovery week will ease me back in
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