I encountered the same problem, but found it easy to fix - I just clicked somewhere before the time limit (just over 1 hour from the beginning, in my case), and chose the "Split file into two" option. I was then able to edit the second half OK. I expect if you have files longer then two hours, you may have to split them more than once.
After I finidhed editing, I joined the files up again (Edit|Select All, Edit|Copy in the second half, End, Edit Paster in the first half).