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It appears that sync servers using a software package called cPanel sometimes (but not always) handle the names of files we send them in a way that other sync servers don't. Bluehost and other hosting providers include cPanel in their hosting packages.

When OmniFocus syncs with a cPanel server, we observe that some (but not all) of the files we upload are processed differently than other web servers do. We send the file with one name, but when the server stores the file, it changes the file name. As far as we know, cPanel is the only server package that behaves this way.
Nerdy digression: Specifically, cPanel appears to sometimes (but not always) URL-encode the file names multiple times. For example, they convert "=" to "%3D" and "+" into %2B". This is pretty normal. What cPanel does, though, is then convert the "%" characters. Other web servers don't do that, because the url encoding for "%" is... "%25". It's actually longer, and contains the character they're encoding.
In any case, OmniFocus for Mac has a workaround in place for this idiosyncrasy - during a normal sync, we reverse their process and put the names back the way we expect them to be.

However: if the database on the Mac gets deleted, OmniFocus handles things differently. We copy the database back down from the server to the Mac, but then we don't apply the cPanel-specific workaround that our regular sync code does. At that point, the file names in the database on your Mac are left in a state that OmniFocus doesn't know how to work with.

We'll add the work around to the "replace my database with the servers' database" code in an update. In the meantime, we've written a script which has (so far) worked to repair the file names without requiring folks with this problem to send their databases to us.
IMPORTANT NOTE: If you are not having this exact problem, please do not run the script. If you're having a different problem, the script may make things worse, rather than better!

If you're not sure this script will help, contact the support ninjas before doing anything else.

(Some folks may remember the "smooshing" script from a few years back; they probably also remember what I'm worried about here.)
If you're having this problem, you should be able to get back up and running by quitting, then using the steps below. If you're not able to sync at the end, contact us and we can help.
  1. Quit OmniFocus.
  2. Open the "Utilities" folder in your Applications folder.
  3. Launch the "Terminal" app in that folder.
  4. Unzip the attached script file, then drop it on the open Terminal window.
  5. Hit return to run the script.

Hope this helps!
Attached Files
File Type: zip FixFocusFilenames.zip (909 Bytes, 383 views)