Someone sent me files into my iPad DropBox account which filled the whole 2gb allocation some 2-3 months ago. Today I get a notification from DropBox team that my allocation is full I need to upgrade. Surprisingly all the files have disappeared from the Dropbox. Does anybody know how I can recover those missing files. How long does Dropbox keep files?

You are probably best contacting DropBox's support. If you files can be retrieved, that's where it will happen.

The only exception might be files in the app that you marked as favorites. They should still be local on the iPad. If you use Open in, or email them you might be able to recover a few.