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If you see them when running reports in Accounts Receivable and selecting the New file, that means that they are not posted in Accounts Receivable. You will want to go to Tasks, Post Entries and review the journal that prints out to see if they are rejecting for some reason. The entries could have an invalid date or be corrupt, or maybe they will post successfully and you'll be all set!
Let us know how it goes!
I've posted, there isn't anything in the new file in AR, but it shows up in the new file in billing I believe. It shows up correctly as being billed (previous work completed) but doesn't show up in aging (contract or customer).
The workflow goes like this: Post the invoice in Billing, creates entries in Accounts Receivable. Post in Accounts Receivable (Often automatic when posting in Billing), entries are sent to Contracts. Billing then pull the Previous Billed totals from Contracts on to the new invoice - so what you are describing is missing a piece to the puzzle. If the invoice is not in AR, it can't be part of the previous work completed, unless it was in AR and was voided, and those void entries did not post to the contract.
I would open Contracts and post, check the report for rejections, then delete the invoice in Billing and start over.