Update: The issue is now resolved. UCS Central supports both SHA-1 and SHA-2 certificates, so that was not the issue. The issue just happened to manifest itself when I was working with the SHA-2 trusted point.
The issue was related to a known bug in the version of UCS Central we are running (v1.3 1b) - Symbolic links not removed correctly when managing Trusted Points. Details of this issue and the workaround (manually unlink the broken symbolic links from command line) are here: https://bst.cloudapps.cisco.com/bugsearch/bug/CSCuy14299/?referring_site=bugquickviewredir
This issue is resolved in v1.4 (1b).
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