I found out the hard way that opening a database in Designer 8.5.3 can recompile all the code in the Java source folder, even if the 'Build Automatically' is unchecked.
So if you open a database that is in use, it might crash the database with:
07-12-2011 13:13:10 HTTP JVM: java.lang.SecurityException: Error verifying signature for resource WEB-INF/classes/xpages/Demo.class. For more detailed information, please consult error-log-0.xml located in /data/notesdata/domino/workspace/logs
After that the only way to get the database back online is to clean the database in designer.
If you plan to open databases in designer on production servers (not even modifying anything) or work with multiple people on the same database, setting the preference to not recompile xPages automatically will save you a lot of grief (or your job).
 7 December 2011  comments (2)
Vince's
Ramblings.
Recompile code when opening in designer (xPages)