LSP: Unused suppression comment warning disappears after first edit

Flow version: v0.117

## Expected behavior

Given the code:

```flow
// @flow

// $FlowFixMe
const lol = 1 + 1;
```

...line 3 should have an "unused suppression comment" warning because there is no error on the next line.

## Actual behavior

The warning shows up when the Flow server first starts up, but immediately disappears after the user edits and saves the file. It never reappears.

More info at the GItHub project below, which contains a tiny project w/ .flowconfig that reproduces the bug.

* Link to Try-Flow or Github repo: https://github.com/jvilk-stripe/flow-unused-suppression-comment-bug