I've created an invoice query that filters by payment date and project. When I apply this to the Invoice History report, the invoices that were allocated to multiple projects show the entire amount of the invoice and payment rather than just the part pertaining to that project. Does anyone know how to fix that so it only shows the part relevant to the project I filtered by in the invoice query?

Try this, go to GL, Reports, then Account Reports, then General Ledger Reports. I filter on projects, select the one you want, and then, if you just want to see invoices, filter on Journals and select AP as your source. This will show only the AP entries into the project you select.