For our applications we need to support two versions of a 3rd party application. The vendor offers DLLs - one for each version - to do so.
I used this SO answer to make it work for the MSI version of our application. The ClickOnce configuration, however, seems to be impossible. It looks like ClickOnce doesn't care about folders and just adds the two DLLs to the manifest (different version in the assemblyidentity and different hash values). After the download is completed the application isn't starting, because the identity of one DLL cannot be verified.
I am assuming that the two versions cannot be distinguished an therefore the wrong hash value is used for the check.