Don't make any changes within SH3 commander mid patrol. You can do it before a patrol, or after a patrol, as long as your U-boat is docked at it's home port when you make the changes.
You shouldn't have the sky issue again as long as you avoid making changes to SH3 Commander mid patrol.
"shouldn't" being the operative word
EDIT:
if you plan on using JSGME to install mods (or installing mods by any method really)... make sure you utilize the "roll back" feature in SH3 Commander before doing so. this will remove any of the small changes SH3 Commander made and prevent problems and crashes.
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