If Work Folders is being really really rubbish then move to OneDrive.
If thats not an option then try and defrag the Database:
Defrag the Work Folders sync database
Check the size of the metadata (meta.db) on the Work Folders server. If it’s over 500GiB in size, I recommend running defrag on the database.
The meta.db is located on the same volume as the Sync Share. For example, if the Sync Share is on the D: volume, the meta.db would be located under the following path:
To defrag the database, perform the following steps:
Stop and disable the SyncShareSvc service (so it doesn’t start)
Run the following command from an elevated command prompt:
esentutl /d <DRIVE>:\SyncShareState\syncsharename\metadata\meta.edb
This command will defragment and compact the database.
Once the esentutl operation completes, start the SyncShareSvc service