This is of course a serious bug if it depends on KiCad itself. But it needs to be demonstrated repeatably. Otherwise it’s impossible to find the reason and fix it.
See New icons in nightly if you are interested in opinions. KiCad already has possibility for runtime custom icon sets: icons are in a package, images.tar.gz, which you can change. But creating an icon set is a huge task and nobody has made a complete set AFAIK. As you can read in the thread, the old set was problematic because of licencing issues.
Maybe this helps?
Otherwise, can you give the zipped project for us to check?
This is out of scope for the KiCad project, the volunteers are already burdened with other tasks. Maybe someone knows about Ubuntu package history and can tell if the old packages are available for old systems.
The situation on Windows is a bit different, the old packages are for example in KiCad Downloads.
I don’t understand your explanation, but are you trying to modify the “official” KiCad libraries? They are not meant to be modified. That’s why they are read-only. If you need to modify a symbol or a footprint, copy it to your personal library first. If you need new symbols or footprints, create a personal library (in a folder with read/write permissions) for them. That’s how it works.