Create a library only containing color variables. Now duplicate that file, open and modify the values of few color tokens leave the name as is so the same in both files now when you try to replace the color tokens from one or the other file variables with the same name disappear instead of updating.
Hey @smunawar we just got back to you via email!
As soon as we have more details about the specific intent with the feautre, we’ll post an update to the thread. 
Update
Salman was a bit confused a to why the app was deleting the local variables when swapping/replacing those with others from an External Library.
The function is working as intended: since you don’t want to reference the local variables anymore, the app is correctly removing them from the document and updating all links to the ones in the external Library.