Those labels look like a good place to start. sub them out and pass the array.

Those large, gnarly if/elsif clauses would be my next step. Create a descriptively named sub like has_many_valid_lodgements, move the logic there and return true or false. This also has the advantage of self-documenting your code. No one will be able to quickly discern what

scalar(@all_lodgements) > 2 && ($total_all_lodged == $total_qcs_docs)
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Look for copy-and-paste code like the Date_Cmp's. Get rid of them. Make 1 sub and name it well.

Other Notes:

• Think about writing tests, even with the code as it stands. The tests for this will have to be high level but you'll know if you break something (or even find a bug). As you refactor add smaller tests for the smaller components. It not only will keep you from breaking things, it helps you think about refactoring. Refactored code is generally easily tested.
• Think about self documenting the code. You seem to use decent variable names continue that with the refactored subs. Think about leaving your code to someone else, and if they'll like you in the end :)