Flow-IDE seems to be caching errors
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Sometimes, when certain error goes away in Flow, Flow-IDE keeps the error visible. In this first screenshot the error has been fixed but is still displayed by Flow-IDE:

However when introducing another error and fixing that error, the original error can disappear:


When these situations happen the 'cached' error is not displayed when running flow via CLI.
I have noticed this too, but I cannot reproduce this problem reliably. Do you have some code and exact steps to reproduce this that you can share?
It should only ever in theory happen with atom-ide-ui because of it's hacky emulation of the Linter APIs. Which linting consumer are you getting this with?
I use the linter, linter-ui-default, and flow-ide packages.