I'm not entirely surprised that the "Custom" amps were discontinued. I love mine, but there's not really anything sexy about it, no catch-phrasable selling point, no rock star endorsement, it's not the "most this or that" amp around.
If I had to find a way to describe it, I would say it as Paul probably would, it's a reliable tool for a musician, especially a gigging musician. It's got a lot of useful features - two channels, effects loop, solo boost, reverb, bias points, and it hits a happy place of good tone, flexibility, and simplicity. For those reasons, I love it. But, the Archon seems to have surpassed it in terms of popularity (and, if anything, the MT15 and Sonzera are another nail in the coffin), though they're different amps I still think the Archon is eating up a share of what may otherwise be Custom amp sales. I'm very glad to have mine, it's nice to have the option of a more open, vintage voice.
One thing I am left wondering, with the HXDA and Custom amps gone, the only amp sitting in the vintage voiced part of the PRS lineup is the Grissom, and kind of the Sonzera and JMOD - I expect there to be something else to fit somewhere in the empty spots. We'll see, maybe Les will get his other Brit amp...