So I was playing around with my Stonco floodlight with my NOS Advance 100 watt cwa mercury ballast and putting in different 100 watt lamps and on start up of one of the lamps it suddleny started flickering pretty bad and the lamp shut off. I could still hear the ballast humming so I suspected capacitor right away. I bypassed the capacitor for just a second to see if the lamp would light and it did and then unplugged it. My question is, could I have killed the capacitor by swapping the lamps frequently and starting them up? Ive never seen this happen before and it's a bit upsetting

 My 1000 w Wide-Lite did the same thing a few years ago, when i got it it had a bad ballast (core&coil potted in tar) dug it out and replaced it with a used M47/H36 ballast from an old hi-bay. It worked great for about a year, then one night I turned it on and it ran for maybe a minute than went out, tried swapping lamp, nothing! swapped cap with one from another hi-bay and works fine now! so yeah, it's possible i guess

My 1000 w Wide-Lite did the same thing a few years ago, when i got it it had a bad ballast (core&coil potted in tar) dug it out and replaced it with a used M47/H36 ballast from an old hi-bay. It worked great for about a year, then one night I turned it on and it ran for maybe a minute than went out, tried swapping lamp, nothing! swapped cap with one from another hi-bay and works fine now! so yeah, it's possible i guess

Not really related to the thread but is there any way you could get some pictures of your stuff up on here? It sounds like you have lots of interesting things in your collection.

To the title: Yes.

My question is, could I have killed the capacitor by swapping the lamps frequently and starting them up?

No. It was just the capacitor fault alone.
It was likely an internal connection fault - lead wire going to the capacitor spool. The lamp was flickering - that mean the capacitor internal connection was "hanging on a thread" and that "thread" just broke and started arcing (so the flicker), eroding the material further away from the broken  spot. So then when shutting down and reconnecting the power, the connection was lost for good...

lumex, I have a lot of stuff i'd like to share, still working on that, hopefully soon, (yes i've said that a million times before!) not enough time a even less computer knowledge

Yes, a capacitor can suddenly flat out die with no warning.  I've seen it in HVAC installations.