First of all I'd like to thank you for looking after this mod, I've had it on previous versions of KSP though apart from a couple test flight I was mostly lazy and used StageRecovery instead.
I've had an issue today though, installed version 1.2.9.1 on KSP 1.10.1.2939 with a few other mods installed:
I flew a quick test mission with a quick and dirty ramjet plane with a belly hold that dropped a simple probecore-fueltank-engine rocket out.
Mission proceeded in the following order:
I lofted the plane up into a parabolic profile and built a bit of speed
I dumped the rocket out the hold, swtiched to it with ] and then flew it into orbit
I then used FMRS to switch back to the carrier plane which I flew back to base and landed on the runway
I recovered the carrier using the standard top of the screen recover vessel button
As expected this jumped me back to the probe sitting happily in orbit
So far so good, then it was dinner time so I exited KSP (I think I exited to the main base screen before then exiting to the menu and shutting KSP down).
Well on loading up again I find that the two Kerbals who flew the carrier are safe and sound in the Astronaut Centre but they have reverted to level 0!
I had a quick look though the last couple pages and will read back further but thought I'd chuck up a quick post in case someone else has had this before and can chip in with an "Oh yeah, that'll happen if you do/don't do x".
I'm going to also try again with a different pair of Kerbals and see if it happens again.
Cheers.
ETA: One thing I have noticed when recreating the problem is that having got my probe into orbit and trying to return to the carrier is that it can take a lot of clicks on the button to get the revert to stage to trigger. Whether thats related or not I don't know.