The club will face St Mirren in the final of the Scottish Communities League Cup on March 17, but McGlynn insists the rewards of a victory that day will not be enough to move the Jambos out of the red.
The Tynecastle club had to appeal to their supporters for help last year when HMRC issued them with a winding-up order over an unpaid £1.75million tax bill.
A share issue brought in £1.79million as fans rallied to the cause, while the club struck a deal with the Revenue that will see £1.5m repaid over three years.
The club also paid a separate £450,000 bill to the tax authorities just before Christmas, but financial concerns remain with an expected £2million shortfall in turnover that has already affected payment of wages and bonuses to players.
Those delays led to the club being issued with transfer restrictions by the Scottish Premier League and McGlynn knows their problems will not be fixed by their cup final date.
He told Press Association Sport: "I'm not the financial director, so I don't know the exact state of play. However, I would still encourage the fans to support the club by turning up for the games. That is the biggest thing that they can do and there was another big support on Wednesday evening at Dundee.
"But no-one should get complacent with the financial situation at the football club and think that we have cracked it by getting to the cup final. There is more to it than that."
An embargo on signing players was only partially lifted earlier this month by the SPL after settlement of outstanding debts to their playing staff, with the terms relaxed to allow them to bring in players aged 21 or younger, and only on a one-out, one-in basis.
McGlynn was then able to snap up both Danny Wilson and Michael Ngoo on loan from Liverpool, but he was still sufficiently hampered in his pursuit of new recruits as the January transfer window closed on Thursday.
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- Scottish Premier League