Coot might crash on you - it shouldn't.
Whenever Coot manipulates the model, it saves a backup pdb file. There are backup files in the directory coot-backup 1. You can recover the session (until the last edit) by reading in the pdb file that you started with last time and then use File -> Recover Session....
I would like to know about coot crashing 2 so that I can fix it as soon as possible. If you want your problem fixed, this involves some work on your part sadly.
First please make sure that you are using the most recent version of coot. I will often need to know as much as possible about what you did to cause the bug. If you can reproduce the bug and send me the files that are needed to cause it, I can almost certainly fix it 3 - especially if you use the debugger (gdb) and send a backtrace too4. Note that you may have to source the contents of bin/coot so that the libraries are can be found when the executable dynamically links.
[1] COOT_BACKUP_DIR is used in preference if set
[2] The map-reading problem (documented in Section Maps in General) is already known.
[3] now there's a hostage to fortune.
[4] to do so, please send me the output of the following: $ gdb `which coot-real` corefile and then at the (gdb) prompt type: where, where corefile is the core dump file, core or core.4536 or some such.