Copy the database off to some other device, and delete it. (Do all this with HA shut down, of course.) HA will build a new one when it restarts.
There should be more than 2 tables in the database. Mine right now has 13 tables.
If you’re running off an SD card, you should be aggressive about excluding entities from Recorder. As I mentioned above, it’s not just the size (although this is indeed an issue) but also the number of writes. Apparently there’s a lifetime limit on writing to an SD card.
This link should give you a good start toward reducing the size:
For the record, my database right now is sitting at under 23MB. A bit higher than I’d like. I think it would be a lot smaller if I could get rid of all those long-term statistics data I never use.