I solved it myself. I noticed with the ingame-debugger running the rocket was shortly visible and got a message like "was unloaded due to NaN Orbit".
My guts pointed me to the jr decouplers. I had removed the top of them out of the stagging and added the bottom instead before doing a quicksave. I fiddled with the save file and removed both of them from stagging by modifing the save file.
Now the rocket is loading again. Looks to me there is a bug in the software. I assume on loading the game thinks the bottom jr was detached and try to split the vessel than discovers no ORBIT info for the rocket a removed the parts leaving the upper part alone. Odd...