Not able to test a production of that length here, but you might consider breaking it up into smaller sequences (click the + sign to the right of the sequence tab above the time line, at the left, to open a new, blank sequence).
After you've added effects, combine the sequences into one. A sequence can be dropped into another sequence - just like an audio or video clip. To see them, click the SEQUENCE tab in the media area (top-left).
If that doesn't fly, you might export (produce) a sequence, then drop it back as a file into another sequence.
FILE|Save AS your project regularly, using incremented file names so as not to overwrite earlier versions.
