The numbers appeared to me to actually be PD series, the 46C and 42A, which (as you know TwoTired) are from the 78 550K (the 46C) and 77-78 750k (42A) respectively.
So of the two you listed, the 46 is the closest to correct, BUT if by CB550F you mean CB550 Four, then the 46 is the correct carb.
I suspect you are making the common mistake of thinking any 4 cylinder CB550 is a CB550F. On the 550 (and 750) SOHC4, the F is a specific model. The models that originally came with the 4 individual mufflers are K models. The F model 550's had a factory 4-1 exhaust and richer jetting (but otherwise identical engine). The 77 550F uses a different carb than the 77 550K, 069 for the F model and PD46C for the K model.
If you aren't sure what you have look at the VIN tag on the neck. It will say 550K or 550F.