Whooaaaa
Not so hasty
It's an easy piece of software to use once you get the hang of it and it automatically saves backups of the files that it modifies, so apart from clobbering your PC with a hammer while using it there's not too much damage you can do.
Just put JaBBgl in a folder inside your main FS2004 folder - call it something like 'utils' as you never know, if you get the bug you might want to start messing about with other sim-enhancing utilties!
Run JaBBgl (double click the exe file

) and you'll get a nice little panel with 2 panes. In the left one, browse to your main FS9/2004 Scenery folder. Then click to enter the eurw (western Europe) sub-folder.
The first thing you'll see is a scenery bgl called amsterd.bgl (no prizes for guessing that one) but it doesn't contain any useful (this time) data.
Now click on each of the following bgl files and - Voila! - in the right hand pane you'll see all of the airports it contains.
Check each bgl file in turn in the left hand pane until you come to the one(s) covering the Netherlands.
Then click on each airport in turn to edit its elevation data - pretty self-explanatory really how to do it.
Change as many as you want - remember, if the AI wheels are in the ground, lower the elevation and vice versa. You'll only be talking about a metre or so in all cases.
The changes aren't saved until you EXIT the prog and it automatically saves a backup folder containing the files you changed on your desktop.
I rename them 123456.BAK (from 123456.bgl) and put them BACK in the folder from where they came. BUT you can't keep bgl in their names (eg 123456_bak.bgl) otherwise FS2004 still reads them.
Hope this does the trick for you.
Any Mods around? Might be worth keeping this as a sticky as there are regular queries about this problem.
Roger