For our use case we would like to keep data synced to our database, and only retrieve records changed since last import. For this purpose updated_since works great.
But there does not appear to be any way to retrieve which records have been deleted. Which will result in a permanent discrepancy unless we import all records every single time, which seems very wasteful.
Please advise on how we can find records that have been deleted.
Hi there 
Jamie from FreeAgent here, thanks for reaching out. As you say, currently it is not possible to get the invoices which have been deleted, but I can see how this would be really useful.
I’ve logged this as a feature request for you, which means this will get triaged by the correct team for consideration in due course.
Best regards,
Jamie
Webhooks would be one solution to this problem 
Webhooks would be perfect, or even to simplify the development time needed by free agent, a CDC endpoint similar to the QuickBooks API.