I'm always falling for this one so maybe it's a valid answer.
I'm a System Administrator so I see all data but in terms of Role hierarchy I'm not on the top of the food chain; there's "Director of IT", "CEO" etc. above me. When I make a new Opportunity-related report it memorizes the hierarchy and gives me 0 rows in the edit page even with "all opportunities" selected. I need to run the report, click the top Role, then I'll truly see all data in the org I want and can happily go back to crafting and saving the report.
Org wide defaults for Opportunities are "private + grant access using hierarchies", same for Accounts.
I suspect it's something like that because if the report type is truly "broken" you get a more specific message.
Check if any of following has changed:
- admin has disabled "Allow Reports" on custom object (if there's any in the report type),
- filter in report is based on a field that was deleted / user lost the visibility due to field-level security
- master-detail changes (again, that would be only on custom object if there's any in the report type, not on Account-Opportunity link)