TL;DR
Add additional check(s) before overwriting a save file. A good candidate is the map exchange string.What ?
Pretty much what the TL;DR says.Why ?
It is currently too easy to overwrite a different game file when saving and it can cost a lot of time and be really frustrating.Especially when one has saving more or less in muscle memory.
The check for the playtime already exists and helps a great deal, but it isn't enough when playing a save with a long playtime where one can easily overwrite a save with a slightly shorter play time.
An additional check (such as the map exchange string) would be even more safe and can probably be implemented at the same place where the playtime is checked.
It also might not be that much effort to implement.