Update local Database?

I have an overpass server setup locally, which is working, but there's still one more issue I have with it. Some results are different from my server to the public one, and I want to know what the best way of fixing that is? Should I just scrap the whole database and re-download it, following this?

I posted about this previously, and from that I setup daily diffs on my database which solved some of the issues that I had. This was a few days ago, but clearly has not solved all of my problems.

Here's an example query that is producing different results for me:

nwr["name:en"="Warsaw Chopin Airport"];
out geom;

My result (only the first three lines are shown here, and preceding "<" omitted in xml output):

way id="237594029">
bounds minlat="52.1419630" minlon="20.9393671" maxlat="52.1842563" maxlon="20.9878821"/>
nd ref="8857075938"/>

Public server's result:

way id="237594029">
bounds minlat="52.1419630" minlon="20.9393671" maxlat="52.1842522" maxlon="20.9878821"/>
nd ref="8857075938" lat="52.1731347" lon="20.9770425"/>

The difference here is that the node (and many other nodes in this way) do not have a lat / lon in my results. I'm pretty sure this is also the cause of the center of this way being calculated very wrong.

My center:

way id="237594029">
center lat="-19.4078719" lon="-96.8802413"/>

Public server's center:

way id="237594029">
center lat="52.1631076" lon="20.9636246"/>

Any ideas on the best way to update/change/fixing my local database would be very appreciated!