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I am not able to reproduce this using a fresh lmdb database (using schema version 5). Is your lmdb database an older schema which got upgraded to v5? In other words, did you use this lmdb database with a PowerDNS version older than 4.8?
Indeed, creating and populating an lmdb database with 4.7.x, the 4.9.x pdnsutil will only remove one key matching the identifier, rather than all of them.
Short description
Really similar - if not identical - problem to issue #12394 and PR #12322
Environment
Steps to reproduce
I'm not sure how and when the keys were added, maybe before the issue and PR mentioned earlier.
Expected behaviour
Both
to actually delete the keys with id "tsigkey1."
Actual behaviour
Described earlier :
pdnsutil gives a "Deleted TSIG key tsigkey1" message but not taken into account
pdns API gives a "Not found" answer
Config lmdb snippet
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