Your post is not clear. Did you scrap stuff in the settlement first and then increase it by 100%? Then start building to max and then tried to increase it again with no results? There are other ways around build limits. Might be the MA has changed the way this works and put limits in it's use, but I have not seen any references nor discussions. Going over 200% is a bad idea anyway unless you have a powerhouse machine. If you did not scrap anything, and then started building and used one of the high poly items from OCD it is possible you made a jump so high it exceeded the next limit, although unlikely at Sanctuary, it could happen easily in some small limit sites.
I have never had much success using multiple changes unless I reset to default in between, but I never go over 200%. 25% reset then go to 50%, another reset and on to 75%, and last reset and add 100%, but that is it.
If you really insist on going over 200% you can use the gun glitch. Drop weapons on the ground and store or scrap them in the workbench. The yellow bar decreases by the poly count in that item, use at your own risk. Knowing which items in OCD are high poly (you see the bar move when built) and not using them will help you by not increasing the build size as much. I only remember one that I tested with, but the prewar blast radius game only took 10 instances being built in one settlement exceeded the build limit. Years ago I forget which settlement, maybe Oberland.