In case you could use it afterward, I use CueTools to generate a cue sheet out of the previous tracking, so I don't have to retrack the single file later.
Detailed in
https://superuser.com/questions/432074/how-can-i-make-a-flaccue-from-multiple-flac-fileshttp://cue.tools/wiki/CUETools_DownloadThere are some limitations to this:
If your tracked files have SBEs, CueTools will pad them when creating the single file, causing clicks between tracks. That won't happen when joining with shntool/Foobar/etc. so I just keep the cue file that CueTools generates, and delete the single track that it makes. (I always use CDWave so I don't have this problem for my own shows, but I get tracked files with SBEs from friends with Macs, and then I have to do this longer process.)
CueTools will only make the cue sheet from CD compliant files, so if the tracked FLACs aren't in that format, I have to downsample them to create the cue sheet.