As I recall, this is not a TWOS issue, but a SH3-4-5 issue. The SH code is fairly old and does not seem to save all the data. If you saved close to land or ships, it “might” cause immediate game issues and/or corrupt your campaign long term which is why players came up with those tips.
As far as I know, no one managed to fix this problem, although as I recall it was worse in SH3 than in SH4-5. You can save anytime and see what happens, just make sure to keep old saves so you can revert back.
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