The HND project file format is based on the SQLite database format which includes various optimizations to speed-up disk reading and writing operations:

Using the "Vacuum Project" command from HelpNDoc's "Tools" ribbon tab will optimize the currently opened HND project file by rebuilding it and repack its content into a minimal amount of disk space. This leads to smaller and faster HND project files.

Vacuuming HelpNDoc projects should be done from time to time.