Hey @zstoynova, unfortunately, I was not able to solve it. I created a very ugly workaround: two Apache vhost-configs with the same eprints ID and different domains, one of them using mod_substitute to change all links to its domain. The second vhost with the 'false' domain includes this additional lines:
AddOutputFilterByType INFLATE;SUBSTITUTE;DEFLATE text/html text/plain text/cgi
while example.com is the domain known to eprints and example2.com is the additional domain name.