The track has four lights on it. Two lights are controlled seperatly by two switches running to the same track. I am upgrading to LED, and want to only use one switch for the track. Can I simply cap and tape off the extra black and white wires, and ignore the extra switch, or will this cause some other problem, like power continuing through the wires.
There won't be any "extra" wires if you do the job correctly. Currently (I'm guessing), each switch has a hot input and the switched output black wire which goes to the lights. The white neutrals are all tied together somewhere. What you need to do is cap off the hot lead to the switch you're removing (make sure this capped dead-end wire remains inside the box) and move the output wire from that switch over to the output post on the remaining switch. If you're just going to leave the dead switch in-place, then you're done.
If your concern was about leaving that switch "live," then certainly you should not do that (cap the hot lead as I wrote above)
Assuming that both switches are in the same box you can nut them together with a pigtail going to the switch terminal, or if the switch has both a screw down and a push in terminal you can use one for one light and the other for the other light. If the switches are in different locations then you'll have to run a cable from the switch you want to use to either the light or the other box. What to do with the existing cable depends on which location you take the new cable to.