If you decide to rename a certificate in your certificate manager, but then leave the "Rename existing certificate" window by clicking OK and without actually renaming the certificate, that certificate will be deleted from yout certificate store.
I think this is due to the implementation of renameEntry(...) in class de.mendelson.util.security.KeyStoreUtil:
An easy solution would be to verify that newAlias has really changed compared to oldAlias, I guess.
Tested with mendelson opensource AS2 build 55.
thank you for your error report. We could reproduce this in our current version. Seems to be in for some years but nobody has tried to rename an alias without entering a new alias name...
We will fix this for the next version