It's more likely that it's timing out while waiting for the imap server to complete the operation. Instead of sending a mass delete of a bunch of messages, break it up into chunks. Something along the lines of:

    my $msgset = Mail::IMAPClient::MessageSet->new( $imap->messages );

    my $msg_ids = [];

    if ( $msgset ) {
        $msg_ids = $msgset->unfold;
    }

    while ( my @cur_block = splice @$msg_ids, 0, 500 ) {
        # delete the current block of messages...
    }
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Untested of course. Hopefully that gets you going in the right direction.