I've never heard why refitting would cause CTD's, do it all the time. It's possbile saving many times over the same save could cause them, moreso if you save near contacts with lower system specs. Most CTD's are file related to improper mods, residue files leftover, ect. I've played for two years and can't remember the last CTD I had, except when playing with mod files on a seperate game install.
You can refit away, it takes two refits to fill a empty sub with torps and has no effect on points.
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