Absolutely. Tested with default .inis (including a blank skyrimcustom.ini). BethINI creates backups of Skyrim.ini and SkyrimPrefs.ini, but not SkyrimCustom.ini. When the Restore Backup function is used, the original Skyrim.ini and SkyrimPrefs.ini are swapped back, but the tweaked SkyrimCustom.ini stays, populated with all the default BethINI tweaks (and any other changes made).
Obviously unchecking 'Modify Custom INIs' is a workaround if one wants to avoid SkyrimCustom.ini entirely.
log.txt
log.txt