Sharepoint Sites on SP 2010

Just recently on the 23rd or 24th of November we ran into a problem where everyone's "SharePoint Sites" folder on their local PC lost all the shortcuts to their sites.

So we tried the usual remove library and add it back again wait 24 hours etc but that failed to work.

We also noticed that clicking the "Open with Explorer" button to open a library in Windows explorer was now prompting for a username and password. This was never the case previously.

A few days later it was also discovered that opening our OWA through IE when inside our network it was also prompting for a username and password when previously it had never done so. (I don't know if this is tied in or not but thought it might be useful to info.)

Now our SharePoint site is loaded into our local intranet sites in IE so that hasn't changed. We have tried various entries in the registry since our site is a FQDN.

As I say this was working and we didn't need any special registry entries before. Problem is one of our main system engineers has moved on and my knowledge in this area is very limited.

We do have a slightly mixed office environment as we run 2010 but have Skype for Business which is 2013. Does this make a difference? SharePoint sites was working since we had SfB installed.

I was wondering if there was a patch that came out recently that caused an issue. We install patches about a week or so after they are released to give us time to find out if there is any issue. I pulled the whole last round of patches off a PC but this didn't resolve the issue.

I hope that isn't information overload but I've tried to give a bit of background to what has been tried so I don't cover the same ground again. Though I may have missed something :)

Thanks to anyone that can give me any pointers on this problem.