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I have a polygon layer and I have a joined table with a link to an excel document for each polygon. Under the "Display" tab in layer properties I check the "Support Hyperlinks using field:" box and select the joined field that my document link is in and choose "Document" as my link type, apply and OK. It works fine, the excel document opens when I click the polygon with the hyperlink tool as it should. Now when I save the .mxd file,close it and then open it again, my changes to the Hyperlinks are not saved. Any other changes I make are saving, my joined table is still there, but the "Support Hyperlinks using field:" is no longer checked.

Why would it not be saving this?

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There are a number of functions that don't work with joined fields. Hyperlinks (at least with the Hyperlink tool) were and I believe still are one of them. See Esri KB article http://support.esri.com/en/knowledgebase/techarticles/detail/17493 for more detail. You would need to permanently add that field to your table for the Hyperlink tool to work. Alternatively, if the complete URL is in the field, you can use the Identify tool on a feature and click the field in the Identify info box, which should launch the link as it is independent of the Hyperlink tool.

Even if it is working within a session, I suspect that the way data is loaded when you open the mxd isn't seeing the join field when trying to initialize the links, so the setting is removed. Later in the process the join is established and the field present.

It's also possible this might be a bug, though I can't find a reference to it in versions more current than 10.0 as linked above.

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