[Nihl]

Eh, I'm not convinced it's much of an issue.

Khanda always has spoon-like tip, streghtening plates along the sides and a basket handle.

Ok, so does the definition have to remain that way? The point of the proposed dictionary is to help keep everyone up to date with the most recent terms and definitions, so:

that term was used locally for different swords, over millennia, in different localities, religions, languages etc.

We can include this in our definition for khanda then! We can say that colloquially (in modern collector parlance that is) "khanda" usually refers to a basket-hilted sword with a double edged blade blah blah blah BUT that there are exceptions! And if we all agree it to be necessary, then we can list out those exceptions!

Bich’hwa stemmed from Mysore and Hyderabad, but it was called Baku in Kannada and Vinchu in Marathi.

Again, I fail to see how this is an issue. In my proposed format we could simply just write this as:
"Bichwa" Baku (Kannada) Vinchu (Marathi) etc etc...

Some years ago we had a topic on Phul-Kattara and the author changed his definition of it every couple of days.

Unless I'm mistaken, wasn't it determined that the phul-kattara was literally just a katar that happened to have a floral decoration on its scabbard? I might be wrong, but if that is the case then it's simply a super specific subtype, not something to really be concerned about.

The same Firangi from the South became Dhup in Maharashtra and Asa Shamshir up north.

Again, I don't see this as being an issue:
"Firangi" Dhop (Marathi) Asa Shamshir (North Indian Persian/Urdu)
We simply define an item with its most well known term, native or not, and list all subsequent terms after that.

I bet that some swords transported from Adoni to Bikaner changed their names several times along the way:-)

Yes, this is how language works. They didn't "change names" though, they were simply referred to by different terms that meant more or less the same thing. If I am a man and I go to India and someone calls me an आदमी (aadmi), does that mean what I am fundamentally changed in that moment and I ceased to be a man, and am instead an आदमी? No, of course not. These words all operate concurrently with eachother, not in any sort of hierarchy.
The reason why we as collectors and researchers can choose which term to use is because we are at the liberty to do so. We are on the outside, and so we can choose which term to use at our convenience. I, at least, would find it impolite and insensitive to ignore all other concurrent terms and "pick favorites", however, which is why I advocate for including multiple native terms in our definitions; so that readers are aware of this concurrent terminology.

Our books are just scratching the surface and some known names do not even have physical examples: how about Kalachurri?

Then we still give it an entry but state that we do not know its physical form? I again fail to see how this is an issue. You could tell me there was a 12th century central Indian sword known as a "Banana", and that that's all we know about it, and I would still happily include it as:
"Banana" (Native language unknown).
A type of central Indian sword said to have existed in the 12th century. No further information is known about this sword type.

We think that curved swords were brought by Babur, but there were Indian sabers centuries and centuries before that. What were their names?

Then we simply identify these items with descriptions instead of snappy names! Reality is what we make of it, we can always write things as:
Medieval Indian Saber (Native name unknown).
Thought to have existed across India before the arrival of the Mughals, though no examples currently survive and not much further research has been done into these swords.

I, personally, have not heard much about these pre-mughal sabers you speak of Ariel, so that would be an entry you'll have to help me with . I'm aware of several types of medieval swords that existed at least in southern India, but I haven't seen any sabers among them, so really I would encourage you to post some images of paintings or temple carvings if you're able. Either way, just because we don't know the exact autochthonous name for something, doesn't mean we can't define or include it in our proposed dictionary.