Source:
How to reset favourite bar to display in time order - Microsoft Community
Preventive measure:
After organizing Favorites in your preferred order, export one or both of these registry keys every day. Double-clicking (merging) either key will
restore the value (sort order) when the key was exported.
Favorites:
HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Explorer\MenuOrder\Favorites
Favorites Bar (Links)
HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Explorer\MenuOrder\Favorites\Favorites Bar
Exporting those registry keys:
From Start> Run (or Windows logo key + r) type in REGEDIT and hit Enter.
Export/backup the entire registry (for safety)
In Registry Editor select Computer in the left pane then File> Export. Save that REG file in a convenient location. Double-clicking that REG file will restore the previous registry and undo any changes, if necessary.
Then:
Drill down, by clicking the + to
HKEY_CURRENT_USER
Software
Microsoft
Windows
CurrentVersion
Explorer
MenuOrder
Favorites
Select Favorites, right-click> Export.
Repeat for Favorites Bar.
Exit Registry Editor.
So...I am not sure of a way to prevent a user itself how to "not swap" the links etc. however, you can always use your software that resets the computer/workstations every night to go back to this registry figure(s).
There may also be a way to prevent users entirely via the registry but I wouldn't even know where to start with that one.