If you stop the "Windows SharePoint Services Web Application" it will remove all SharePoint websites along with your customizations from IIS!!!
So, Until you are very sure what you are doing, Never stop the Windows SharePoint Services Web Application. In case, it happened already then you have to apply ALL your IIS manual customizations (including Web.config changes, Certificates, IIS Manual changes, etc). This is why Microsoft says "Don't touch IIS".
If you Must restart it, then Take the Backup of IIS Metabase and do it.
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