Where did my Empyrean Merits go?

[Nightmarer 2]

Mmmkay, just logged a couple chars to get rid of Anti-Matter since I have the mish saved and then joined a kill most ITF on one of them. Realized that, despite being vet lvl 12, I only have the last 20 emp merits I obtained during the ITF run so I am missing the emp merits granted on vet lvl 3, 6 and 9, it is 52 Empyrean Merits (used 8 crafting a rare incarnate salvage). Logged the other char I used today after the patch, vet lvl 7and he's only got 2 emp merits instead of 32 (also used 8 on a rare component). 

 

Is this happening to anyone else? I don't dare logging any more chars and no clue what to do now.