A feature for Acrolinx server 4.6 and onwards is most likely causing valid terms to be flagged.
This feature is intended to display flags (by default) for valid terms and their conflicting deprecated terms. In your case, the valid terms should not be flagged, so the feature can be manually turned off.
To do this, please edit the following file:
Add the following line to the file:
Save the file and restart all Acrolinx servers. After doing so you should be able to view the configuration by browsing to the Acrolinx Dashboard > Maintenance > View Configuration. Once there you can follow the path data > en > configuration.properties as per the screen-shot below:
If you don't see the line available in the preview window, it hasn't been entered and saved in your configuration file and you should try again.
This should solve your issue with valid terms being flagged.