I spent the bulk of yesterday re-organising what was my iTunes library into a format more suited to Quodlibet, doing things like sciphoning off non-needed albums/tracks, normalizing and seperating certain values (featuring credits, artists, producers) etc. When I opened it this morning however, the library appeared totally empty, meaning I had to spend needless time deleting the same hundreds of unpredictably placed, untagged bonus tracks I did yesterday. I thought it could be related to the media being stored on an external drive (/media/external/music/), but there's nothing indicating this is the case.

Also, the only relevant option (to retaining the same songs previously added) I can see in the options menu is 'Scan directory', which will only add the problem files automatically, as opposed to my doing them.

tl;dr: I would like a media library that isn't temporary, and doesn't require an hour of work every time I open it or remove my external drive.

Library rescan adds all songs it can find in "scan directory". And if you haven't turned it off, that will be done on every start.
If you want to add songs manually use the "Music > Add folder" (or drag n drop) which does the same thing once.

Regarding external drives (and mount points in general): Library rescan will hide all songs that are not mounted or show them again if the drive has been mounted since the last scan. So, once you mount your external drive, do a library rescan, and all should be there again.

If not, please post the steps of your actions, what you expected and what happened instead.

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It would seem this only happened once. I probably plugged in my external after running QL or something similar.

If this re-occurs I'll bump this topic.