I uploaded my primary music library consisting of FLAC files with attached cue sheet on Kodi and the tracks are played as expected.
Connecting the host to Yatse and using the local player I noticed that the tracks are correctly indicated but whatever the selected song is, the playback always starts from the beginning and the timebar shows the total time of the album
Yes this is unfortunately caused by Kodi limitations that does not return anything except the same flac file for each tracks.
Yatse have no way to have the cue file, no way to know it’s from a cue file and no way to reconstruct the queue file to properly handle everything like the silence positions.