I get this message printed to the console... it seems I have all of the exported data so not sure why. My filters are currently set to *, to export all data... I think.
If I recall correctly, this started with the previous version (2.6?).

https://prnt.sc/Msonhp73qiVD
https://prnt.sc/w62zh-85i2dc
I do not get an error if I use 3 stars.
What exactly have you configured?

All three filters are set to *. I also tried setting only the propertyFilter to * and leaving the first two empty, same results.

DiffType and DiffProtoType are also set to *

So it seems the test if(not prototype) equates to true, prototype being IRawData.getPrototype(typeName,prototypeName).
I am not sure where the values for DiffType (typeName) and DiffPrototype (prototypeName) come from. I see they are runtime values, so I assume they are assigned.
I noticed in the code, their default values are "" and not "*".
So I tried hard coding the values to be "" inside the diffPrototype function, but then I just get ERROR: prototype / not found.

I do have your Base Prototype Data mod installed but never populated it, if that could be the issue.

   4.232 Script @__Kux-RawDataProvider__/modules/RawData.lua:66: RawData.filterList
{
  ["*"] = {
    ["*"] = {
      ["*"] = {}
    }
  }
}

Edit: Base Diff is not enabled.

Edit 2: And please, do not lose sleep over this, not a big deal.

This is the problem
DiffType and DiffPrototype does not support * this must be an existing name
because you can only diff one prototype at the same time with its base

EnableDiffPrototype is being set to true, still looking around for where/how that occurs.

On a side note, I just noticed common..cfg, probably meant to have just a single .

Very interesting issue. If I add my add my own runtime-global (in the second data:extend in settings.lua) and assign it a default value, it retains the value I set.
However, EnableDiffPrototype changes from false to true, DiffType to * and DiffPrototype to *.
If I add settings.global[mod.prefix.."EnableDiffPrototype"].value = false just before the if, EnableDiffPrototype still has the value of true.

Never mind, ignore this entire issue (except the common..cfg). I am at fault, sorry to have bothered you.
I did not understand runtime-globals were the map settings, kind of embarrassing.

The issue is always 50cm in front of the monitor ;-)
The Diff feature is intentionally in the map settings and not at startup , because it is not necessary to restart the game to use it. In principle, I could make a own GUI for it, but I haven't needed it that often to make it worth the effort.