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I have the problem documented in this post:

The file size of my OmniFocus file has now grown up to 3mb and it's
resulting in it loading slowly on the iPhone and syncing slowly. I've
decided to export the file from OmniFocus to the desktop and then use
this to replace the OmniFocus file in ~/Library/Application Support/
OmniFocus/OmniFocus.focus and this has resulted in the file reducing
to 36kb. It opens super fast again on the iPhone and syncs really quickly.

Is there any way to prevent this being necessary? I have tried the
advice in the forum post above and this does help, but not to the extent
that i need it to and it's not long before the size increases out of
control again.

Thanks in advance