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Make sure that the running copy of OmniGraffle has a license available -- Go to the licenses panel via the OmniGraffle menu, and if it claims that there is no license available, then another copy of OmniGraffle is using that license key somewhere on your network, causing your copy to run in demo mode, limiting the editing of files to those with fewer than 20 objects.

If your copy of OmniGraffle is licensed, all you need do is open up the Graffle files in question using a text editor (OmniGraffle documents are XML), perform a search for the string, "ReadOnly" (minus the quotes) and change the key value from "YES" to "NO" in each case (again, minus the quotes) and save.

Hope that helps,
"Vroom! Vroom!!"