The help files present in the Help folder are erased during a Developer Update. This is due to the fact that the entire Help directory is deleted, then recreated, and that the help files are not under version control. The html help files are generated from the aida sources when the application is built, so indeed they should not be in the repository (the aida source files are).
The solution would be to preserve them somehow during a checkout and reinstall them when it is complete.
This is fixed.
Changes committed to the repository (rev. 1227 (sourceforge.net)).