ignoreFilterIfFieldNotInIndex setting should only affect the queries that are sent from dashboards, and shouldn't be messing with any of your data. So if you were to turn this setting on for testing purposes and then turn it back off, it shouldn't have any lasting effects on your Kibana instance. The only behavior it changes is which filters are applied to visualizations in your dashboards.
There was recently a bug with this setting not being correctly applied to visualizations, which was fixed as of
6.7. The issue description sums up the purpose of this setting nicely:
ignoreFilterIfFieldNotInIndex should prevent visualizations on a dashboard from being filtered if the index pattern they're based on does not contain the filtered field
There are still some remaining issues with the setting; to ensure it is working for you as expected, I'd suggest reading the discussion on this issue first. Then you could try turning it on temporarily -- perhaps in a separate Space with some sample data if you want to avoid affecting other users of your dashboards -- before permanently toggling it on.
Hope this helps!