WARNING: Database migration history has been reset on this release. That means that the SQLite database will need to be rebuilt.
The best way to do this (in my opinion) is to move the SQLite DB to another location. (It was previously named Server.db by default, but is now Remotely.db by default.) Upgrade the Remotely server and restart it. A new database file will be created automatically.
Now open the old DB in DB Browser for SQLite (a free and open-source program). Export the database to a SQL file, choosing only the tables you need (typically Devices, DeviceGroups, Users, and Organizations). Choose "data only" for the export, and keep the insert statements.
Now import the SQL file to the new database. Click No to create a new database, so it imports into the existing one.
There may be errors due to schema changes, which will need to be resolved by modifying the SQL file (for example, adding additional column insert statements). Rinse and repeat until the import works.
As Remotely gets closer to leaving beta, there won't be anymore breaking changes like