The data is generated up using ST2 XT2 and references the wav/wma files.
If you remove the other wma and wav from the folder and back them up elsewhere it will just have empty items in Reaper with missing media
and only load the media that is there. Biab may or may not get an error, you can just try.
You can only write cue points into wav files, once done in wav you can then write them in flac as take markers but these are not stored in the flac file only in Reaper. You can create a midi file of the same name with chord markers that can be stored in the RealTrack folder, if you then load both files into reaper the midi markers can be transferred into the flac/wma file as take markers. Both cue points or midi markers can be copied from an item as Regions or Markers.