Nel played 65 minutes in Edinburgh's win over Harlequins on Saturday after missing games through a neck complaint.
Another Edinburgh player, Rory Sutherland, is also ruled out through injury, but the squad includes five players from the English Premiership despite a row over funding that led the clubs to vote to stop them appearing for their country.
Captain Greig Laidlaw, Moray Low, Duncan Taylor, Sean Maitland and Tim Visser have all been included for the games against Australia, Argentina and Georgia.
The dispute - which is also threatening to withhold English based players from Samoa, Italy and Tonga - arose over an outstanding injury bill of 400,000 pounds with Premiership Rugby Ltd.
Cotter believes the dispute will be settled.
"That is an executive issue and (Scottish Rugby Union chief executive) Mark Dodson is dealing with that at the minute, so I'm not sure where it's going to get to," the New Zealander said.
"But we are anticipating having the players available to us, so I will let the whole thing unfold over the next couple of days, then we will know a bit more."
Cotter said the games represented a chance for those selected to shine.
"This is an important season for this group of players who are determined to be successful in a Scotland jersey, and have a clear will to win.
"We have a big emphasis on how we play in front of our home crowd and have three exciting challenges facing us this November."
Scotland play Australia at BT Murrayfield on 12 Nov. before facing Argentina at the same venue and Georgia at Kilmarnock’s Rugby Park on the following Saturdays.
Squad Forwards: Allan Dell (Edinburgh), Alasdair Dickinson (Edinburgh), Zander Fagerson (Glasgow), Moray Low (Exeter), Gordon Reid (Glasgow); Ross Ford (Edinburgh, Fraser Brown (Glasgow), Stuart McInally (Edinburgh); Grant Gilchrist (Edinburgh), Jonny Gray (Glasgow), Richie Gray (Toulouse), Tim Swinson (Glasgow); John Barclay (Scarlets), John Hardie (Edinburgh), Rob Harley (Glasgow), Josh Strauss (Glasgow), Hamish Watson (Edinburgh), Ryan Wilson (Glasgow).
Backs: Greig Laidlaw (c) (Gloucester), Henry Pyrgos (Glasgow); Pete Horne (Glasgow), Finn Russell (Glasgow); Mark Bennett (Glasgow), Alex Dunbar (Glasgow), Huw Jones (Stormers), Duncan Taylor (Saracens); Damien Hoyland (Edinburgh), Sean Maitland (Saracens), Tommy Seymour (Glasgow), Tim Visser (Harlequins); Stuart Hogg (Glasgow)
(Reporting by Neil Robinson, editing by Pritha Sarkar)
