ok I had a look at it. Correct, manually disabled sets are not taken over.
If you single click a set in that list, cmpro's settings file only holds index information about the enabled/disabled set, not its name. So restoring is only possible when you quit/restart cmpro with the same profile. Updating will reset this, since it's very likely that the index have changed.
But there is still a way to achieve what you want...
Either you can specify your selection in the "select sets" input field (supports regex/variables...that in combination with the "invert and initial invert" buttons should handle mostly everything. So you can for example select "%f=005;%f=yard;" plus invert/initial invert to disable 005 and yard.
...or...(if that edit box gets too messy...or too long)
Edit a textfile where you list the set names (1 set per line) which you want to exlude..for example
005
yard
Save this file somewhere, go to set information, browse for that file in "from file" and hit "load", then the listed files are enabled. Hit "invert" and the sets are disabled, since this invert action is a 1-time-only action, and you want to invert your selection all the time, you need to enabled "initial invert"....and you're done.
Both should survive a datfile update