Well... it shouldn't... but, it probably depends on your broker. I would ask them if I were you, who is your broker?
I've had some issues with Interactive Brokers recently, where I had plenty of funds but for some reason after hours trading messed things up... and I got margin violations, even when I didn't have a position anymore... and after 3 days (3 margin violations) I could only close positions... which I didn't even have...
All sorted out now.
So... best to check with the broker.
Also, if you have some things in writing... like when they say "even if you get margin warnings, we won't liquidate immediately and we will first look at total position and funds"... that way you've got some kinda fall back position when they actually do liquidate and you might be able to recover some...