I want to replace two switches controlling one track with one
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)