I'm going to assume you are using the Unlocked H2EK. I've got a few tips on which executable to use. There are certain edits to a scenario that will corrupt the file upon saving:
H2 Guerilla - UNLOCKED & EXPERT MODE
Make sure you are using the Unlocked H2 Guerilla from here: H2EK Unlocked
This unlocked version of Guerilla allows you to view/edit previously locked tags and to create
new tags of various types.
H2GuerillaDONE.exe -> Use for normal unlocked editing.
H2GuerillaTST.exe -> Use for editing otherwise hidden fields such as object naming, improved
scripting support and messing with cameras.
H2GuerillaNEW.exe -> Same features as the TST version plus it will not corrupt a scenario
tag when adding Kill Trigger Volumes or weapons to a Single Player scenario. Of the three
editors mentioned here this is the most stable however it can only open one scenario at a time.
A work-around to this is opening a second or third instance of H2GuerillaNEW as required.