The answer is yes, you can repair a linoleum floor. You take a scrap
piece from your installation and a relatively coarse file and make a
pile of pulvarized linoleum. Then add a small amount of wood glue and
use the paste to fill the hole. Getting the color right is a bit
tricky, but since most linoleum has some random variation, you can
probably get close enough. The varnish is actually polyeurethane, and
the floor guy I talked to said we have to live with it and hope it
wears off over time.