ReplayGain

[simbun]

Are you sure you didn't apply the Gain to the actual music itself?

The only reason I ask is that you said "recoded (3 years ago, maybe) my entire collection flac -> flac" and then you said it took 5 hours for batches (and gave 1000 tracks as an example). I've also heard that the language around ReplayGain used in DBPowerAmp isn't very clear.

Analysing the music just to add the tags REPLAYGAIN_TRACK_GAIN and REPLAYGAIN_TRACK_PEAK (and album if required) should not be taking more than 10 seconds or so per album, unless of course you're running on a very slow CPU and running it over a very slow network.
Using foobar I scanned 200 tracks and it had finished the operation in 50 seconds. I know you can use different algorithms to calculate the track peak which can massively affect the speed of operation, but I can't install DBPowerAmp to test as Replaygain is behind a pay wall (and I used a trial license a few months ago to try and rip a copy controlled CD).

One way to check would be to use CUETools to verify one of your previous rips.

Apologies if I'm barking up the wrong tree.

EDIT:
I performed the ReplayGain operation over the network on 477 files and it took 5m 20s. If you chose to write the file out to another location, or if the source had to be rewritten because of insufficient padding, this would have also increased the duration.