using qaac64.exe, musicbee isn't able to split + convert some image + cue files

[BuzzyOrange]

I've been trying to setup the Ipod & Iphone Driver plugin for a few days now - THIS PROBLEM ISN'T RELATED TO IT - but when converting on the fly to transfer tracks with itunes, it gets complicated. For context I'm working on windows 10 with musicbee version 3.5.8698.
My first problem is that some image + cue files don't get splitted as instructed. Most of the time the images are in flac. Sometimes it tries to sync the non-splitted file, sometimes it splits it in files that get synced 50/50. Other times the files split, maybe, but won't sync, I imagine because they're too large but I don't know really. Sometimes files that were synced properly before don't sync anymore. Something that happens all the time though is that when the sync fails, musicbee leaves a large temp file in appdata/local/temp folder. Those files accumulate and since qaac seems to always go through some temp file at this location to convert, it "plugs" the syncing process as other files end up not having any temp space to get converted.
I'm adding two other issues here that are kinda related :
Tried syncing using a filter, worked with a "belongs to playlist" filter, didn't with a "doesn't belong to playlist" one.
Tried changing a cue file manually to get different metadatas on songs in the library by "scanning folders for new tracks" afterwards or deleting the current files before that (with notepad++, inb4 I didn't forget to save). Doesn't work, only using the "edit cue sheet" button does anything (along with editing metadatas by hand of course) and it updates the files I'm working on in notepad++ so it's not a path error or something, maybe a cache thing ?
Sorry if my English isn't very clear, hope you can understand what I'm talking about.

[The Incredible Boom Boom]

Tried changing a cue file manually to get different metadatas on songs in the library by "scanning folders for new tracks" afterwards or deleting the current files before that (with notepad++, inb4 I didn't forget to save). Doesn't work, only using the "edit cue sheet" button does anything (along with editing metadatas by hand of course) and it updates the files I'm working on in notepad++ so it's not a path error or something, maybe a cache thing ?

This was the only part of your message I semi-understood.

When I was testing whether to use CUE + single files for my library, the only edits that stuck in MusicBee were ones I made in MusicBee. I think I also encountered multiple issues with edits being reverted if changes to the single file were made. I concluded that using a cue sheet to hold all the tags I "require" was not the method for me. If you only want basic tags to be applied, they may work for you, but otherwise you may have to accept the same conclusion I did.