Did you use the Analyzer (actually a Duplicate Finder) and ‘Batch’ delete everything that it found?
If so then you will almost certainly have deleted some duplicate files that the Windows System needs, and some duplicate files that some apps need.
Having already done the damage your options now are:
If you have a current system backup, or a Windows restore point, then you can try restoring that to get the deleted duplicates back again.
It will depend on just what type of backups you make. They should be in a full System Image, but probably not in a Data/Files only backup.
If you don’t have those, or they don’t work then running DISM and SFC should repair the Windows system.
If you are having problems with any particular apps then you may need to repair/reinstall them, depending on if the app has a repair option or not.