Hmm seems I was a bit too quick. Flashsfv is a gui thing and isnt that handy for commandline useage. Luckily my ftplogger is verifying sfv files as well and is working well on a commandline. I'm going to release a small program called recurse.exe which will simply recurse through a dir and perform a command. Kinda like:
recurse *.sfv c:\ioftpd\scripts\ftplogger.exe %1
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