The SH series has had the corrupt save bug since SH3. If you have ships nearby, you don't save the game. If you are not on the surface, you don't save the game. Being underwater or having the enemy close often results in a corrupt save.
But there is a difference between a corrupt save and an app crash.
You need to go mod by mod and see which one causes the issue.
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Good Hunting!
Captain Haplo
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