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I think that what you may be seeing is that one lemmy server can only see the comments that are transferred to it. That happens when:

• The second server is federated with the first (which is the case here)

• Someone on the second server has subscribed to the community on the lemmy instance in which the comment was made prior to that comment being made.

Otherwise, lemmy.today will never know about the fact that another account you have somewhere posted a comment somewhere else.

It's part of what lets the Fediverse scale up, because not every server has to have every comment made somewhere transferred to it. But...yeah, doesn't help with visibility.

My guess is that someone will make a search engine that tries to slurp up the whole Fediverse's comments at some point and make them searchable, if Google doesn't get there first. Gopher had people index it (Veronica). Usenet had people index it (IIRC altavista, then Google Groups until whatever happened that made it not searchable any more). The Web had people index it (Google, Bing, a zillion others). All it takes is someone with the bandwidth, storage, CPU time, and some way to fund it (showing ads or something?).