I tested on a new Steam install of KSP 1.12.3, without any mod except ModuleManager 4.2.2, Harmony, and KSPCommunityFixes 1.23 (all installed from CKAN), and StuckOnLoadingPartUpgradesFix 1.1 (installed from the Github release).
Test case:
Create a new sandbox game
Create a rocket in the VAB and change some attributes of the part (for my test case, I put a RoverMax with the non-default gold skin and a Mk1 Pod with the lights on and the flag mirrored)
Launch the rocket
Quicksave
Quickload
The RoverMax has its default white skin, the lights of the Mk1Pod is off, and the flag is no longer mirrored
Exit KSP
Remove KSPCommunityFixes folder
Restart KSP, load your sandbox game, load the existing quicksave
All the parts are loaded properly with all their attributes (so the bug is not in the saving process but in the loading process)
Exit KSP
Re-add KSPCommunityFixes
Removed StuckOnLoadingPartUpgradesFix files (2 files and 1 folder)
Restart KSP, load your sandbox game, load the quicksave
All the parts are also loaded properly with all their attributes
The bug affect all modifications you can do with the little attribute popup, whether you do then in the VAB/SPH or during the flight, and whether it's a stock attribute or a mod attribute (originally I found the bug because of TweakScale: on load, parts have their default size)
There is an interaction going on between StuckOnLoadingPartUpgradesFix and https://github.com/KSPModdingLibs/KSPCommunityFixes
I tested on a new Steam install of KSP 1.12.3, without any mod except ModuleManager 4.2.2, Harmony, and KSPCommunityFixes 1.23 (all installed from CKAN), and StuckOnLoadingPartUpgradesFix 1.1 (installed from the Github release).
Test case:
The bug affect all modifications you can do with the little attribute popup, whether you do then in the VAB/SPH or during the flight, and whether it's a stock attribute or a mod attribute (originally I found the bug because of TweakScale: on load, parts have their default size)