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I've added some configurable debug logging that will show up in v48.0.94931
(I just committed it, so it'll be a while before it shows up in the download list).

You should be able to do the following in Terminal:

defaults write com.omnigroup.OmniFocus OSUDebugDownload -bool YES
Then, launch OmniFocus and do a software update. There should be some logging
in /Applications/Utilities/ that will maybe provide a clue as to where
this is going wrong.

Once you've gathered the logs, you can do:

defaults remove com.omnigroup.OmniFocus OSUDebugDownload
to make the logging stop.
CTO, The Omni Group