I have been having the same(ish) problem. If I revert to VAB at launch or after launch, all of the parts of the rocket spawn underground and cannot be selected to bring them up again. The only solution is starting over. Even opening saved vehicle files can spawn stuff below the floor. If I revert to launch site, the everything disappears from staging (except the staging groups...with nothing in them) and cannot be started. The only way to get it functioning again is quitting and restarting.