Let me start from the bottom...
Template X is a generic template which has discovery rule defined, it contains a few items (all snmp) na graphs in it. Template Y is linked to X and this one is used on hosts. Hosts are monitored by proxy (which probably is irrelevant at this time). After adding a few items to the discovery rule in template X I found that the new items are not being created on the hosts. Only unlinking with clearing and then relinking the template seem to work but that is not an option since I have 300 devices with that template and I'm not prepared to loose the gathered data. Please repair it because it renders lld quite useless.