This also happened to me yesterday. When I checked again a few hours later they were back, so I didn't report anything. However, after checking it a few different times this evening they seem to have been removed again. I should have Bronze Mastery (47 wins) and Silver Points (55).
Yes, the match play trophies reset back to zero every time you play a non-match play round.
Kind of like how the personal best long drive and putting gets reset to zero after the end of each round.
They need to fix these 3 simple bugs.
Thanks for the reports.