To create a new database see
this guide. Once that database is created you can import hands into it via 'Play Poker > Get Hands from Disk'. Depending on the number of hands you want to keep this import may take some time so you would want to schedule this to start at the most convenient time as you cannot import manually and use PokerTracker 4 on live tables at the same time. If required you can break the import up into smaller chunks/folders and build up the database gradually.
With regards to the hand histories themselves you can import the original files from
your 'Processed' folder (which you can access via the "File -> Open User Data Folder" option) although if you play tournaments and have manually entered a large number of tournament results I'd recommend exporting the tournaments from the original database where you entered the results and this will create summary files, which contain your manual results, and you can import those instead of the original hand histories.
Incidentally if you have manual player notes you want to keep then you can export/import those via the 'Database -> Notes' menu option. Finally if you are happy you have everything you need in the new database you can go ahead and
delete the original database to get that disk space back.