I just experienced an unexpected behaviour when using MuseScore 4.0.1 to test the portablization of its content folder in DOCUMENTS (see topic below).
After launching it several times to observe the diractories handling, I found MuseScore having adapted some settings from the local install, I used a few weeks ago. That did not happen after the first relaunch but on the second or third one. As far as I can tell, it kept at least the recent files list.
The only action I took before was opening an existing MuseScore3 file from another folder, changing settings to other directories and saving the file as mscx-folder.
My local MuseScore is kind a of vanilla so I cannot say for the other settings at a first glance. I may investigate this further when I have some spare time this sunday...
PortableApps version 4.0.1 and local installation alongside but on different drives, both standard paths.
I did some testing and with the first start, everything was back to normal again. MuseScore local has and keeps its own settings and MuseScorePortable does the same. I could not force my setup to reproduce the "bug" I experienced before. I consider that a one time quirk - maybe a runtime problem with overlaying registry handling or something else. I did not have another Qt-app running at that time that could possibly have interfered, but never mind. I keep an (half open) eye on that.
Digging further in this topic, I found the cause for my misinterpretation - apparently the migration routines from MuseScore4 itself. I think, they kick in after the first launch and my observation was simple conincidence. I had the same files open in the local MuseScore4 as I had in MuseScore3 Portable I used alongside before. i just was confused because they were not there at the first start.