Offset, count, and total are wrong for some queries. _offset produces short pages, and repeats results on different pages

[StevenXLi]

Our SQL queries can return a single resource id more than once.
During the "async" cached path, we track every prior id in a search result, and discard duplicates.
But during _offset queries, or when a client uses the _total=accurate parameter, this de-duplication does not happen.
This problem shows up as a few bug reports reporting either short pages, duplicate results, or incorrect totals.

Steps to reproduce the behavior:

1. Create 5 Patients
2. Create 20 Observations for each patient with code=sample
3. Query _has:Observation:patient:code=sample&_offset=0&_count=5
4. fewer than 5 patients in the bundle

Expected behavior
all 5 patients in the bundle.

Environment (please complete the following information):

• HAPI FHIR Version 6.2.0
• OS: MacOS
• Browser: chrome