First of all, this is not an advice. I do not guarantee anything, this is just a solution that worked for me and that I want to share. Always backup before you do anything and be sure you know what you are doing. I am in no way responsible for your failure or dataloss. Proceed on your own responsibility.
There is currently a bug in IOS 10.3.1 - 10.3.3 that prevents you from deleting Safari browserdata:
One of the more infamous is a bug which stops users from clearing their Safari browsing history and data. This is a problem for all sorts of obvious reasons and has hundreds of complaints spread across two major Apple Support Community threads, among others. It has now persisted through four successive iOS 10 releases.
If you try to remove the website data, some cookies with zero data (0kb) will return.
I searched for a solution on the Internet but I could not find it anywhere. Even on the Apple support pages there are a lot of people with this problem but no-one has found the solution.
Time for me to investigate!
Cookies are just simple text files that are stored on your computer/iphone/ipad. It is always a good idea to clean your website data so tracking cookies will be removed.
So how do you remove the cookies from your iPhone?
Using the interface of the iPhone does not work. Your iPhone does not allow you to delete anything.
That means you have to do it manually. Luckily I found an application that allowed me to browse and edit the filesystem of my iPhone. The application is iMazing:
iMazing, was able to make a copy of a recent backup of my iPhone. With iMazing you can edit the files in the backup. This means you are able to delete the cookies from the backup and do a restore to your iPhone without these empty cookies. After a restore, your website data is clean again!
in this screen of iAmazing you can see the copy of the backup that I edited and that I restore to my iPhone.
The files I deleted to solve the problem:
Browse with iMazing to:
I deleted everything in this folder and the problem was solved!
That's it. Simple or not?