It shouldn't take that long. I have faced the same error after upgrading from 7.3/PU12 to 8.0/PU15.
One reason can be obsolete data entities on the list.
Please run this query in the SQL server to find all obsolete entities on your entity list:
select * from dmfentity where entityconfigkeyname = '' and entityisenabled = 0
Then remove those entities from the Data entities list and try to refresh again. I simply removed all data projects and data entities.
For me this didn't help, but after installing the latest platform binary updates the refresh succeeded. I think there's still something strange in the (local) development environment - I had to restart IIS a couple of times and start the refresh again. But eventually the entity list got refreshed. In our Sandbox tier 2 environment the refreshed works perfectly after the platform binary updates.
