Ok, so I did some testing myself using a dump of Monster Slider that matches redump.org database. First, redump.org does preserve multi-indexed tracks in the .cue-file. Converting this to .cdi before updating Rhea firmware, the multi-indexed tracks (containing various one-liners) are played beginning to end, and subtitles on cutscenes freeze during this. After updating firmware, nothing changed, so I went back to Discjuggler and altered some settings. Specifically, checking both PQ and R-W made the game run properly, picking one-liners from within tracks during gameplay and having proper dialogue in cutscenes that are synced to subtitles. I conclude that Discjuggler is able to properly regenerate subchannel data from the .cue-file given proper settings. This should give working images of all games with multi-indexing.