Under certain conditions, $reindex attempts to index a deleted resource

[lmsurpre]

Describe the bug
After upgrading to 4.6.0, I invoked $reindex and got back a response similar to the following:

HTTP/2 200 
content-type: application/fhir+json
date: Wed, 10 Mar 2021 22:15:41 GMT
content-language: en-US
content-length: 189

{"resourceType":"OperationOutcome","issue":[{"severity":"warning","code":"not-found","diagnostics":"Failed to read resource: Observation/177febab121-84e989ff-17d5-4854-b151-0c482b2d3eb5"}]}

Upon further inspection, we found that this resource is actually deleted.

To Reproduce
Unknown

Expected behavior
The $reindex operation should not attempt to reindex a deleted resource.

Additional context
We've seen this on two separate occasions now, but the root cause needs investigation.

[lmsurpre]

I've run a bunch of reindex commands since this fix went in, and have yet to see the issue again. Lets call it resolved.