If you want to reencode your files (to lossy formats) in the future and keep their metadata stored with the master files, I would recommend to use a lossless format that is taggable. WAVE files with tags or your approach using Cuesheets may work to a certain extent, but this is an old format with many known limitations and/or low support (as you already experienced).
Personally I use tagged FLAC files in my master library and transcode them to lossy formats like MP3 or OPUS for my portable devices whenever I need them (using FFmpeg which copies most of the tags by default).
This could be done every time a new version of the encoder is available without losing quality over the iterations, although I haven’t seen the need to do that so far – encoders don’t evolve as much as they did in the early days of MP3.