The Windows Installer Cache, located in c:\windows\installer folder, is used to store important files for applications installed using the Windows Installer technology and should not be deleted. Same statement applicable for Exchange server and other hosted application. If the installer cache has been compromised, you may not immediately see problems until you perform an action such as uninstall, repair, or update on a product. When a product is installed using Windows Installer critical files are stored in the Windows Installer Cache (default is C:\Windows\Installer). These files are required for uninstalling and updating applications. Missing files cannot be copied between machines since they are unique.
So it is highly recommended to not clear/delete/move Windows Installer Cache from default location. Because these caches has an associated registry key on the server and its hard to determine and correct each and every missing .msi cache.
Now, if you think we can clean the reg key to avoid failure during action such as uninstall, repair, or update on a product. However that will cause more issues than you may expect and you will have to rebuild the server/box.
The only way we can fix this is by copying all missing .msi caches from setup media or healthy server and place it in the installer directory. Challenges are to re-associate these caches with registry.
There is no easy way to re-associate these caches with registry and it would not be wrong saying its equal to impossible. Because you wont be able to identify all missing or required caches and each time we fix one .msi cache it may through an error for another .msi cache. Fixing .msi caches one by one will be time consuming and time will depend on the count of missing .msi cache. Finally you will take a decision of rebuilding the server/box and performing recover server. Recover server will be a time consuming task.
Summarizing, If files are missing from the Windows Installer Cache, you will have to rebuild the operating system and reinstall applications.
Third-party recovery: Some third-party entities claim to be able to rebuild or repair the Windows Installer cache. For legal and supportability reasons we cannot recommend or endorse any of these entities. If you use such third-party products and recommendations you do so at your own risk.
If you have backups for your system prior to the file deletions here are some options:
Full system state restores are required. It is not possible for example to replace only the missing files from a previous backups.