@JimmXinu, I actually went ahead and implemented it myself because it was something I really wanted to see for a long time. It also works flawlessly on my end, so for courageous people I'll attach it below. There was no easy and obvious way for it to work like I wanted, so I had to implement it as a device plugin that monkey-patches the built-in "Kindle 2/3/4/Touch Device Interface".
There should be no problems when Calibre updates, as long as there are no not-backwards compatible changes to the API.
To install it first disconnect your Kindle, disable the built-in "Kindle 2/3/4/Touch Device Interface" plugin in the "Device Interface plugins" section and then install my mod. After that simply restart Calibre.
Here is the code for anyone curious. As I said, I'm not responsible for any damages that it might cause -- I can just state that it works on my end.
And to clarify again: Using this simply allows you to keep your current reading location along with other metadata when you update a story with FFDL while using a Kindle or somehow else cause its UID to change. For example you are reading a story called "XYZ" and are currently at location ABC. Now usually when you would update the story with FFDL your current location would be reset, your highlights would disappear etc. -- using this they don't.