Firstly, a caveat. I'm only running a very early beta of v4.04, but that gives me an insight into how this should work.
My only concern is that whenever V4.04 is released and I install it, my databases are not overwritten between the actual installation of V4.04 (once I have inserted my own NavData db3 file) and having to make a selection to opt out of Auto-Update in "Preferences" each and every time I start my RadarBox.
I'd be surprised if that were the case. I would expect that if you have the "Auto-Populate Aircraft Data" option unticked in v4.03, then that will still be unticked after updating to v4.04:
And as in v4.03, these options are remembered between sessions in v4.04.
All that the installation of v4.04 does is add some new fields to the aircraft table, one being the AUTOUPDATE field, which is set to "Y" on all existing records. And if you have the "Auto-Populate Aircraft Data" unticked, even records with AUTOUPDATE set to "Y" don't get updated when running v4.04.
But even then, a mass update of the whole aircraft table would only occur if you press the "Start Update" button in the new database explorer.
I hope I've explained that clearly. I don't think you need worry that installing v4.04 will suddenly overwrite all you manually edited aircraft records.
Anyway, back to beta testing!!