There are multiple folders in databases, which ones do I delete?
Using the "Rebuild and Rescan Data Bases" option from within Armory should achieve the same thing... Just make sure you have updated to the latest version of Armory as Holliday suggested. Armory 0.96.1 will NOT work with newer version of Bitcoin Core (I think since Bitcoin Core v0.15+ from memory).
However if you want to be REALLY sure that the databases are being done from scratch... delete ALL the files here (assuming Windows):
C:\Users\YOURUSERNAME\AppData\Roaming\Armory\databases