Are levels after 40 cap but before beating Keener lost?

I hit 40 several days ago but was waiting for a friend before taking on Keener. In the meantime I "leveled" many times, getting the familiar orange flash, but I didn't notice any way to track those levels in the stats.

I assumed upon beating Keener, I'd unlock the post game leveling process and the levels I'd gained while capped would transfer over. But after beating Keener tonight I'm only SHD level 1, and see no indication that I leveled at all over the past several days (even though I probably spent 20 hours playing after hitting 40).

Are those levels gone, or am I missing something?

Levels gained at 40 do not transition to SHD levels. In that sense they are lost, so if you're 40 but have not beaten Keener, do not expect any XP earned to go toward the post-campaign leveling system.

However, presumably they do still give specialization points (I did not receive these as I was already capped) and the chance for apparel cache keys.