Premiership clubs had voted to withhold players from international duty over alleged outstanding injury bills.
Captain Greig Laidlaw, Matt Scott, Tim Visser and Sean Maitland are among the Scots playing in England's top flight.
A Scottish Rugby spokesman said: "We are in positive talks with PRL and expect our players to be available."
Australia, Argentina and Georgia visit Scotland in November and head coach Vern Cotter names his squad on Tuesday.
PRL is also reported to be seeking remuneration from the Italian, Samoan and Tongan unions.
Scottish Rugby expects to have all England-based players available for the autumn Tests, despite a funding dispute with Premiership Rugby Ltd (PRL).