This is a known Meta-side issue right now, not your setup. Comment automations have been firing inconsistently across every platform for weeks because Meta's comment webhook delivery is intermittent. ManyChat has acknowledged it and escalated to Meta, but can't fully fix it on their end until Meta does.
A few things that actually help in the meantime:
1. If your automation sends a public reply to the comment AND a DM, those are two separate Meta calls. The public-reply one tends to break first and can silently kill the whole flow before the DM ever fires. Try a version that only sends the DM, no public comment reply, and see if it holds up better. This is probably why editing and duplicating didn't help, the broken public-reply step carried over.
2. Where you can, use a DM keyword automation instead of a pure comment trigger. DM triggers have been more reliable than comment triggers lately.
3. Account > Help > Refresh Permissions clears it sometimes.
For the 50+ that already piled up, most tools have no catch-up so it's manual, unless you're on something that can retroactively scan the post and DM everyone who commented while it was down.