Best practice is to separate updates. What I mean by that, is to perform a sync/update of the official repositories first, and only after that has completed (and often a reboot also), then update any foreign packages you might use (from the AUR, flatpak, appimage, etc).
This is also noted in every Update Announcement topic.
A common example might be; with pacman:
sudo pacman -Syu
(updates packages from the repositories)
and then using pamac:
pamac update --aur
(rebuilds packages via the AUR)
and then;
flatpak update
(if you use flatpak sources)
Yes, electron… sometimes they can get in the way, but generally adopting the above mentioned habit can help avoid those annoyances.
Multi-booting with Windows is unlikely to affect your icons.
The main concerns include ensuring that Windows Fast Startup is disabled, and avoiding Linux tools on NTFS filesystems (only use chkdsk from within Windows to check/repair NTFS).
Also, keeping Windows and Linux in sync with the realtime clock (RTC) takes a simple but necessary tweak to the Windows registry.
Now, after all that I’m afraid I’m not an XFCE user (I use Plasma) so any direct help I can offer is limited. But we have many members who do, so hopefully the wait won’t be too long.
Regards.
Again, not related to your issue, but as you’re multi-booting there are a few noteworthy considerations in a tutorial I authored a while ago; perhaps some may be useful for reference. Cheers.