OK, I'm confused. If I've got a M, T, V, W, or L fare class and upgrade to C or F, do I get an EQM bonus? I didn't think so, but if that's the case, I'm owed a few miles.
Here's my EQM breakdowns for the year:
Total EQMs: 55001
M, T, V, W EQMs: 16994
Y EQMs: 9212 x 1.5 = 13818
F, C EQMs: 17409 (all were upgrade fares from Y, M, T, V, W, or L fares via miles, 500 milers, or CR-1)

For the year, my F & C EQMs got me an additional 6780 EQMs. If I should have gotten the 50% COS bonus, I have been shorted 1925 EQMs.
Also, knowing that upgrading will yield me additional EQMs will make my run for 1K quite a bit easier.