URL rewrite broken after Exchange update

After installing Exchange 2016 CU9, most of our websites stopped working and we are getting the error:

Access denied. You don't have authorization to view this page.

We also noticed our web.config file was missing data and the url rewrites were also gone in IIS. We tried restoring the web.config file from a backup. It did bring back the url rewrites in IIS, but we are still getting the access denied error when trying to browse to the website.
IT MeetjeslandAsked:
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how many websites are there in IIS? Just exchange sites or other websites?
IT MeetjeslandAuthor Commented:
We have some custom websites. We just found out the websites can be accessed on the IIS server itself, but not from another PC in our network, or outside our network.

OWA works with no problem.
AmitIT ArchitectCommented:
Do you have BIN folder backup. If yes, just restore old folders from the backup and copy/paste them in the right path. If you don't understand, what I am saying, open case with MS.
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IT MeetjeslandAuthor Commented:
Ok this is pretty weird. Now our websites are only accessible through https, in the past this was only http, we could not get https to work. This is all fine of course. We still have one issue with logging into one of our websites, we get the error 'Could not connect to server. Please contact the administrator"

The website is running a vtiger customer portal on a linux CentOS.
AmitIT ArchitectCommented:
Is this an Exchange Server or Web Server. As I am not clear, why you have created sites on Exchange.  That will surely screw up the Exchange server. As an Exchange admin, you need to keep it clean, as much possible.
IT MeetjeslandAuthor Commented:
The exchange server is also the ISS server. I know it's not ideal, but this is the situation as it is now.
AmitIT ArchitectCommented:
As per my experience, whenever you install any Service pack or CU for Exchange, it removes all custom sites. And you need to recreate and reconfigure them again. Normally, I take all backups and screenshot. So later I can compare and fix anything changes. In your case, if you have all details, just reconfigure missing pieces and you should be good.

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IT MeetjeslandAuthor Commented:
Issue is resolved. We made a http to https url rewrite setting and had to disable require SSL on the default website. Everything works now.
AmitIT ArchitectCommented:
Good to know, as I said, you need to fix missing pieces after CU upgrade. Going forward, just take the screenshots for all custom sites. Or Move all these site to new server and leave Exchange alone with default site.
AmitIT ArchitectCommented:
Closing this question. Any objection, pls let me know.
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