Synchronization issues can occur for a number of reasons. OmniFocus is storing updates to its database in a number of small files. Should one of these files get lost then it can happen that OmniFocus on the Mac no longer matches with the state of FocusGTD.
In such a case do the following:
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Synchronize all clients (under the assumption that OmniFocus for Mac and iOS are still in sync) and make sure that they are up to date (otherwise non-synched tasks made on iOS might get lost)
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In OmniFocus on the Mac, select File->Move Old Data to Archive
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Select File->Replace Server Database... which will replace all data with the server with data from OmniFocus on your Mac
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And choose "Delete Database"
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Synchronize FocusGTD again
If this did not help, please check this article.