short answer:

using web "facilities" to insert certs did not work on N900 (nor do I expect on N9/50)
copying certs manually to /var/lib/aegis/certs/common-ca will also not work


I would go like:
download cert in pem or convert into pem
put it wherever you like
and install it with /usr/bin/acmcli to common-ca (will need to dig for exact command...)
possibly c_refhash (as you already found out)
--edit
you might do it in as root with devel-su
AND possibly in "develsh" (giving some more rights), as I do not expect you to run that device in OpenMode?


P.S.: what I do not understand on N9/50 is why we have
/var/lib/aegis/certs (/common-ca)
and also
/etc/ssl/certs
Both seem to have the same certs installed (with different hashes/links)? So possibly we need this here, too?