After taking a closer look at my Inquisitor & to a lesser degree my Sage, There is some companion wierdness.
Initially I thought they had been completely removed, but it's stranger than that.
https://imgur.com/a/eS60WoU
Sorry about the hatchet job with ms paint, but basicly my class companions (the ones I did alerts for) are listed twice.
At the bottom as unavailable (dropped out of contact)
AND: the ones i've interacted with are listed a second time further up the companion list with their choices reflected, such as the Andronikos romance being resumed.
My dead theron can also be summoned & is standing in my command centre as well, his character info reflects that I left him behind too which makes it even wierder.