It's not OS dude, trust me I've been using windows phone with WhatsApp for a long time now. I change phones phones quite often and every time I either have to reflash or reset my phone all I had to do is to backup WhatsApp messages to the SD card and backup the WhatsApp folder from under the Photos folder.
What you could have done is:
1) backup your WhatsApp data to SD card from within the app, no copy paste required yet.
2) create a folder named "temp"on the SD card and backup the Photos >> WhatsApp folder to it.
3) check that your WhatsApp messages backup exists on the SD card >> WhatsApp folder.
4) uninstall WhatsApp and clean temporary files using the storage app, by this time WhatsApp will have 0 storage on your phone.
5) configure new images and videos to be stored directly to your SD card from storage sense.
6) install WhatsApp on main memory again.
7) during setup it should prompt you to restore your backup from SD card >> WhatsApp. This will restore all your messages.
8) move the "temp" folder image files back to photos >> WhatsApp.
9) everything should be setup again for future use.
As i mentioned earlier WhatsApp is taking less than 100MB space in my phone memory whereas 3GB media space on my SD card
Well My friend, being an android user I am not used to this kind of shuffling, this is surely windows fault. WHatsapp stopped support for phones running windows before v8. Think there is an issue. I can send documents in android thru whatsapp and in windows it hasn't got updated yet. This clearly shows how windows phones are lacking in software issues and market. There are very less apps and all those cloned apps for example ES FILE MANAGER are full of ads, and does not work. It is also a security threat. I can not see whatsapp folder, videos, audios, pics in the sd card or in the phone storage by the official FILE app or via PC connectivity, Why? Do they think I will make changes to any file of whatsapp there? This is not a user experience I want. To solve a problem in windows you have to search a lot and then take help from forums and somehow you understand that you can do things but with limitations. Google is way better in user experience. Even the so called W10 delayed a lot that I lost hope that it will be present this year. Even that has more problems then W8.1. It will take a decade for windows to make a mark or a good developer to change it's future. Require a person like Pichai.
Issues I faced
1) Mentioned above about whatsapp folder not showing in phone storage or in sd card.
2) Not many apps, most of the apps are cloned by few idiots who put ads in there and those apps don't function, ex- es file manager, mx player etc.
3) No google app (People are more addicted to google apps because of it's simple UI, better support, quick bug fixes), Windows maps seriously does not holds good.
4) If I make a folder in sd card outside the basic folder, and put pics or videos there, they won't show in gallery. (Formatted the phone and SD card thinking that It must be because of SD card.)
5) Faced few lags, require restart sometimes when double tap wake feature doesn't work (It happens around once a month).
6) Can not delete videos by selection in gallery. (How can I delete the whatsapp videos without selection when the folder is also not visible in sd card or in phone storage also)
7) Things gets boring after sometime with not much in it to do.