Hearts enter this weekend's match at Ross County - their final fixture of a tumultuous year - in ninth place in a congested SPL table.
With Hearts' financial woes well publicised and players entering the final six months of their contracts, McGlynn could see many of his established first-team players depart next month.
Australia international Ryan McGowan has been linked with a move, while Scotland defender Andy Webster and captain Marius Zaliukas, a third defender, are all out of contract come the end of the season.
McGlynn described McGowan's link with a move to Asia as "pure speculation".
"Players like Ryan McGowan will attract attention," McGlynn said. "They're out of contract in the summer and the football club is not in a position to knock back good offers if they come in.
"Some players will probably go, if not in January, then at the end of the season.
"We're going to have to go through a transitional period right now and another one in the summer. That's how it will be.
"I would like as many players to stay as possible because that would give me the best chance to do my job best.
"I wouldn't want to lose defenders because that's probably the strongest part of our team, but it may be that these are the players that are sought after most by others.
"I just need to deal with that issue as I have done with every other issue."
Historically Hearts majority shareholder Vladimir Romanov has not allowed players to depart on the cheap - goalkeeper Craig Gordon left for Sunderland in a £9million deal, for example - but the club's dire economic position might dictate moves.
McGlynn returned to Hearts from First Division Raith, where financial constraints were tight, and knew circumstances would be difficult at Tynecastle, but nevertheless believes he can still achieve his aims.
"I came here with the expectation to be in semi-finals and to be competing at the top end of that table; it's kind of living up to expectations," said McGlynn, pointing to the Scottish Communities League Cup semi-final with Inverness on January 26.
"This is probably the most difficult time for Heart of Midlothian Football Club. I don't think they've ever had a transfer embargo in the past or been so close to a winding-up order.
"It's a big challenge. This is a great football club and the players have been fantastic, it's just a wee bit bad timing."
McGlynn was earlier in his career in caretaker control at Hearts after George Burley's departure and believes the chaos of that spell prepared him for this one.
McGlynn, whose hopes for 2013 include a League Cup final place and the hope that eases the financial burden, said: "If we have to put more younger players into the team then fair enough.
"That was my brief - to come here and try to bring through young players."
McGlynn had no update on Hearts' challenge of the indefinite transfer embargo imposed by the Scottish Premier League, but did reveal trialist Arturas Rimkevicius has returned home, for now.
As well as the Dingwall match, Hearts have the Edinburgh derby to look forward to ahead of the winter break.
Should results go their way, Hearts could go above Hibernian, currently fourth, entering the two-week hiatus - and that is a target for McGlynn.
"Ross County will be in a buoyant mood after their victory at Easter Road, so that will make it a tricky game for us, but one I still believe we're capable of winning," he said.
"If we can do that we'll move on to the 28-point mark and if by 10 o'clock on January 3 we have 31 points then I'll be happy."