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Since changes may be stored in fairly small batches, that number of transaction files isn't something I'd worry about too much if you're using the app on several devices. (You're seeing the zip file count go up in the morning because OmniFocus *never* deletes a change file that's less than an hour old.)

I use OmniFocus on two Macs, an iPhone, and an iPad (running both iOS apps). All the apps have been synced today, and I currently have 240 change files on my phone.

If you start getting particularly slow syncs on a regular basis, that's the point at which I'd begin to worry. With the conditions I mentioned above, it takes my phone about 5 seconds to sync over WiFi...