After upgrading Flux to 2.6.x, bootstrapping with SSH auth can fail with 'ssh: handshake failed: knownhosts: key mismatch'. Fix: get the ECDSA host key with ssh-keyscan -t ecdsa and update the known-hosts secret, the maintainer confirmed this resolves it. The underlying fix also shipped in source-controller (PR #1828), so updating Flux past that release is the durable fix. Rolling back to 2.5.1 is only a stopgap.

_Source: gh:fluxcd/flux2#5385 (Flux CD)_