Fairly certain this is the answer to your question. If you aren’t regularly using Trainerroad, whether that is via plan builder OR Train Now, 2+ weeks without a TR workout within any of the zones will lower progression levels. I’ve seen that happen with my VO2 PL’s in the midst of a SS block.
EDIT: to add a bit more to my original comment… at this time, all the other WO’s and rides you are doing in the OTHER apps will only be taken into consideration with regards to how AI FTP detection works within TR. When Workout levels V2 comes along (whenever that might be), all those WO’s in the other apps will leveraged by adaptive training and the PL’s, so what you are currently experiencing shouldn’t be a concern any longer.