I think that's what is so awful about this whole visa situation - you just don't know what to do for the best.
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Did you check with the agent if they had any backlog before you sent them?
When are you due to travel?
I think if it was me and we were travelling within the next month or so, I'd be inclined to ring the agent and check with them and ask when you're likely to get them back.
Good luck
Polly