XRECODE

This is OK as File.flac and file.flac are the same for Windows.

you could calculate suffix based on lowercase filename and attach it to initial filename. in case i described it would help.

There's already setting for that - https://imgur.com/oVw3NXA

yes, i know. but xrecode doesn't add suffix for pair "file" and "File", because names are different. to calculate the necessity to add suffix program should convert filenames to lowercase and if suffix is necessary add it to initial filename.
but such situation could hardly happen in reality, so you could ignore it.

Fixed in the latest beta version.