Hello,
There is a bug when you open some files (ABC) generate MD5 keys then save ABC.MD5 file. Now you open clear ABC files and add DEF, generate keys and save file. The file ALWAYS saves to ABC.MD5 not DEF.MD5 as expected. Even if you try 'save as'.
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Thanks for the report, I'll fix this.
Sorry it took so long to respond, I've not been able to put time into this project in past months (mostly due to WinMerge releases).