I came to understand this when I first ran Roon and was experimenting with my album artwork and metadata vs. the Roon-supplied equivalents. I had been OCD about metadata for years before I used Roon, during which period I primarily used Synology Audio Station (and, secondarily, an Auralic box, which I never truly loved). Upon my first import, I was terribly disappointed at the album artwork quality that Roon displayed, and I wanted to use my own meticulously-curated artwork, so I switched the setting and re-scanned, and within minutes, I was much happier. So that’s how I discovered that.
You are correct; if you set album or track preferences, they will not be overwritten by a rescan.
If you want to convert, say, a 2 CD set to two distinct albums, there are three approaches:
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If you are doing an import for the first time, set all the metadata right for each of the two discs on a work computer with a metadata editor, put them in the right folder structure, and then move them to your Roon watched folders. Done.
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If you have already imported a 2 CD set and want to convert it into two separate albums, the easiest thing to do is what you have outlined. That is:
a) remove the albums from your library;
b) rescan;
c) use the “Clean up library” function; and
d) go to step 1 above as if you were importing anew.
The disadvantage of this - and some may consider it quite minor - is that you will lose all play history for that music.
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If you want to keep the play count & history, however, you can do this, which is cumbersome, but it truly does work (I just did this about a week ago with a Bert Kaempfert album, BTW):
a) Copy your existing 2 CD set from your Roon music source to your work computer to make your metadata and folder structure changes that you desire to make it into two distinct albums;
b) In your Roon music source, delete the old bundled set, then copy the new individual albums to wherever they need to be.
c) Do NOT clean up your library, but DO perform a force rescan. The old album will still look like it is there, which will be frustrating. This is because Roon uses a certain fingerprinting technique when importing your music, and the old library metadata that you did not clear out will make the new files look like the previously deleted ones.
d) When looking in Roon at that old album, select “…” in white circle
e) In first screen, under “Missing or extra tracks,” select “Fix Track Grouping”
f) It will give you an error noting duplicate track numbers or names, which I don’t specifically recall, but it’s OK to do what it suggests
g) At the top of the left column, select “Edit Discs”
h) Deselect all but disc 1
i) Make sure that you only have tracks for disc 1 selected in the right column.
j) At the bottom right, select “Create Album” (1 disc, X tracks or whatever is right)
k) After this, if anything is left on the left hand side, “Remove” it.
l) Then exit the interface, and go back to the underlying album as if you were going to listen to it
m) The album may be “Unidentified” - go back in and identify it (select “…” in white circle, identify album, as usual)
n) The second album should now be separate, and it may need to be identified, too
So there are three other options. But - and I may be wrong - I don’t think that these are really the issues that @Mark_Sealey was facing?