@magico13 After having the crew of a few missions disappear. I managed to track down the cause to StageRecovery(using V1.6.5) and can repro it easily.
Send a crewed ship to either the Mun or Minmus. Then setup a sub-orbital flight with Kerbin that has a SOI change. Which typically happens to me when doing a course correction when matching planes with Minmus.
Then switch to another vessel and then switch back. The crew should then be deleted and marked as dead/missing in the astronaut complex and in the sfs file.
I don't receive any notification of their death, but I do lose rep. Other than that this is a great mod.