Running second cue list in background

yes, you can make a second cuelist and you can make it Phantom, so it will not change your command line or your PSD. but still, somehow you will have to trigger it. so you would either have to press another go button or you add those cues to the first list as well so you can have always the same go button.
when concerned about tracking: are you using your console in tracking mode or cue only? because if using tracking, having "empty" cues in your main cuelist should not change anything.

If your video computer is able to send MSC (for example QLab does), you can trigger the console from the video. Have done that several times.
Why don't you want to have the 50 blank cues? As Uelli said, it won't affect the the output, and it's done in a second in blind.
(In blind: cue xx.01 thru xx.50 enter enter Numbers as you like them of course ).

Thanks guys. I guess I didn't mention what I already knew I could do.
I already knew I could create a second cuelist and run it on a separate fader without effecting the main cue list. Not ideal cuz the board op still is pressing 2 different buttons.
I also know I can just put in the "empty" cues in the main list. It's not about me not wanting to add the cues because either way I'm adding them somewhere. It was more about the lighting desingner and video designers not communicating about their cue structures and how they would interconnect without changing cue numbers on either end.
My designer seemed to think we could just link from let's say LXQ30 to LX 30000 or 2/1 for the video cues and then at some point linking back to LXQ31 but I know that gets messy and linking to a second cue list on the master fader will override the main cue list. I guess I was just trying to make sure there wasn't a third option of linking to the second cue list on the master fader without overriding the main cue list.

You can use {Execute} to run a cue on another cue list without changing what's on the master playback. It can still get messy.

i wouldn't suggest linking across cuelists, but executing cues across cuelists.
linking into another cruelest will get messy i guess. but with execute you can get (empty) cues from another cruelest to fire. that would be my solution to get two communicatively handicapped designers in sync.
don't execute cuelist 2 from cuelist 1, that would mean that the numbers need to be the same. but let's say you have cue 21 as regular lighting cue, then you need 10 video cues before LX22 that has real stuff in it. so you add 10 empty cues 21.11 through 21.20. Cue 21.11 execute cue 2/13 enter. that means when you press go (still on the one big go button) in the background video cue 13 will be triggered.