The issue is caused by the certificate existing in the CDS, but due to the non-alphanumeric characters, it will not show up in the Siteminder Administrative UI.
1. Run XPSExplorer with elevated privileges
2. Take note of the following two menus: Under CDS: Certificate (should be option 3), and under FED: Certificate (should be option 27). These are in alphabetical order by section, so just make sure these two menus are investigated.
3. Choose option 3 - Certificate, then type "S" to Search Objects. This will list all of the certificates that are in the CDS. It should show the Aliases under the Policy Store Object ID (OID), so you should be able to find the cert in question, example: "cert-example"
Important!: Take note of the OID, as you may need to verify it later in the FED menu, as it does not show aliases in that list.
4. Type the number on the left that corresponds to the cert to select it and move to that specific certificate menu i.e. if the cert shows something like the following:
(I) Alias : "cert-example"
Then type "29", and hit enter
5. On this next screen, you will have the option to choose "D - Delete Object". Type D, then hit enter.
6. This will bring you back to the previous menu of certificates stored in the CDS, the cert will likely still show up in the list, but simply type "Q" to quit back one more menu, then type "S" to search objects again, and you will see that it is removed.
7. Go back two menus, and select option 27 - FED, and verify that the certificate is also removed from this menu.
8. Go into the WAMUI and import the certificate manually, making sure to import it with an alias with ONLY alphanumeric characters. This should now succeed, and you should be able to view the certs for usage in Partnerships, etc.