Add IsDeleted check in search queries

[feordin]

Description

We do not have a check for resources being in the deleted state on search queries. This can result in deleted resources being returned in result sets under some conditions.

Related issues

Addresses [issue #3920]. DevOps [issue AB#121553]

Testing

New E2E test added.

FHIR Team Checklist

• Update the title of the PR to be succinct and less than 65 characters
• Add a milestone to the PR for the sprint that it is merged (i.e. add S47)
• Tag the PR with the type of update: Bug, Build, Dependencies, Enhancement, New-Feature or Documentation
• Tag the PR with Open source, Azure API for FHIR (CosmosDB or common code) or Azure Healthcare APIs (SQL or common code) to specify where this change is intended to be released.
• Tag the PR with Schema Version backward compatible or Schema Version backward incompatible or Schema Version unchanged if this adds or updates Sql script which is/is not backward compatible with the code.
• CI is green before merge
• Review squash-merge requirements

Semver Change (docs)

Patch|Skip|Feature|Breaking (reason)

[LTA-Thinking]

Is there a way to write this test using tags? I don't like relying on us never using the Flag resource type in the future, it looks like it could cause hard to debug failures down the road.

[feordin]

I did think about that, but I can't use the tag value later to search, because the resources will be deleted, and the tags should also be deleted at that point.