FULL PRODUCT VERSION :
java version "1.6.0_20"
Java(TM) SE Runtime Environment (build 1.6.0_20-b02)
Java HotSpot(TM) Client VM (build 16.3-b01, mixed mode)

(Issue is also present in Update 18 and Update 19.)

ADDITIONAL OS VERSION INFORMATION :
Microsoft Windows XP [Version 5.1.2600]

EXTRA RELEVANT SYSTEM CONFIGURATION :
Reproduced problem in a VMware Workstation 7.0.1 virtual machine running Windows XP Professional with Service Pack 3.  Issue is also evident on live workstations with Service Pack 2.

A DESCRIPTION OF THE PROBLEM :
With Java Runtime Environment Standard Edition 6.0 Update 18, Update 19, or Update 20 installed, performing a repair or reinstallation from the .msi source installation database causes the majority of the files in the JRE's program directory (%ProgramFiles%\Java, by default) to be deleted, leaving Java unusable on the workstation.  Update 17 does not exhibit this behavior, and a repair or reinstall does not delete core Java files.

The difference appears to be in the RemoveFile table ( http://msdn.microsoft.com/en-us/library/aa371201.aspx ) of the Windows Installer database file.  In Update 17, most of the rows in this table have a value of 2 (msidbRemoveFileInstallModeOnRemove) for the InstallMode column, which means the corresponding files will be deleted upon uninstall.  Since Update 18, however, almost all of the rows in this table now have a value of 3 (msidbRemoveFileInstallModeOnBoth) for the InstallMode column, which means the corresponding files will be deleted when either an uninstall or an *install* is being performed.  This explains the undesirable behavior of core Java files being deleted when a repair or reinstall is being performed.

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
1. Install Java Runtime Environment in interactive mode with a full user interface.  Note that this issue also occurs if Java is installed in unattended mode with a basic or reduced user interface.

msiexec /i jre1.6.0_20.msi /qf

2. Either reinstall Java by running the above command a second time...

msiexec /i jre1.6.0_20.msi /qf

...or repair Java with the following command...

msiexec /f jre1.6.0_20.msi



EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
A fully-functional installation of Java should be present on the workstation with none of its core files having been deleted by the reinstall/repair.
ACTUAL -
If reinstalling, all of Java's program files are deleted from %ProgramFiles%\Java.
If repairing, all of Java's program files are deleted from %ProgramFiles%\Java and only the following files remain in that directory:

jre6\core.zip
jre6\patchjre.exe
jre6\zipper.exe
jre6\bin\msvcr71.dll
jre6\bin\regutils.dll
jre6\lib\ext

REPRODUCIBILITY :
This bug can be reproduced always.

CUSTOMER SUBMITTED WORKAROUND :
Installing Java using a Windows Installer transform that changes the InstallMode for the appropriate rows in the RemoveFile table from 3 back to 2 allows for a repair or reinstall to be performed and complete as expected with no core Java files being deleted.  However, using a transform in this manner would likely cause problems with future versions or Updates of Java.

Release Regression From : 6u17
The above release value was the last known release where this 
bug was not reproducible. Since then there has been a regression.