FULL PRODUCT VERSION :
java version "1.8.0_60"
Java(TM) SE Runtime Environment (build 1.8.0_60-b27)
Java HotSpot(TM) Client VM (build 25.60-b23, mixed mode, sharing)

ADDITIONAL OS VERSION INFORMATION :
Windows 7 64 bit
Windows 8.1 64 bit

EXTRA RELEVANT SYSTEM CONFIGURATION :
Tested with an without a previous version of Java installed (Java 7 or 8)

A DESCRIPTION OF THE PROBLEM :
Our software saves a licence key in a subkey of HKEY_LOCAL_MACHINE\SOFTWARE\JavaSoft\Prefs. After installing Java 8 update 60, we found the entire "JavaSoft" registry key was deleted so the licence was removed.
After repairing the software to replace the registry keys, Java 8 update 60 was uninstalled.
However, this simply removed the registry key again!
It seems the offline installer will always do this on install, but the web installer can upgrade an earlier version without issue. However, uninstall still removes the registry key.

REGRESSION. Last worked in version 8u51

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
1. On a Windows machine, add a registry key to HKEY_LOCAL_MACHINE\SOFTWARE\JavaSoft\Prefs if it does not already exist.
2. Install Java 8 update 60 JRE using the offline installer. The registry will be deleted: HKEY_LOCAL_MACHINE\SOFTWARE\JavaSoft
3. Re-add a registry key to HKEY_LOCAL_MACHINE\SOFTWARE\JavaSoft\Prefs
4. Uninstall Java 8 update 60 from the Windows Control Panel.
The registry will be deleted: HKEY_LOCAL_MACHINE\SOFTWARE\JavaSoft.

Note: in a test, using the web installer to upgrade an existing version of Java 8 did not delete the registry. However, uninstall did then remove the key.

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
Installing/uninstalling Java 8 JRE should not delete HKEY_LOCAL_MACHINE\SOFTWARE\JavaSoft.
ACTUAL -
Installing/uninstalling Java 8 update 60 JRE deletes HKEY_LOCAL_MACHINE\SOFTWARE\JavaSoft.

REPRODUCIBILITY :
This bug can be reproduced always.

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N/A. Use standard installers and manually create registry keys.
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CUSTOMER SUBMITTED WORKAROUND :
None found. Do not install!
We have to reinstall our software or restore a back up of the registry.