hard to say when we cant see the mod itself, post as a coment the mod XML and maybe i can help you. Even tho i am new to modding, ill do my best to help you out. ;)

Let's say I simply copied over the vanilla xml from Gameplay\XML\Misc\CivBEHealthLevels.xml into the mod and tweaked some integers. Everything appears fine, but has no effect in-game. I did enable the "updatedatabase" action in the mod, and tried including the modded file into the VFS. Still, nothing.

Oh the health bonuses and debuffs area. You use ModBuddy?

Yes.
Anyway, SOME values can be replaced using
But this doesn't work for things like "healthstart" and "healthend", and makes the game ignore the whole file instead.

yea i have found myself with the same problem when making my mods. Is like the game has its limitation depending what area you are trying to modify. But what you cant do in one area, you can do it in another area.

For example, i have been unable to make a building that gives 1 unhealthy, but i can, instead, make it give me 1% unhealthy...

Because the comand <Unhealth></Unhealth> doesnt work on buildings... But <UnhealthModify></UnhealthModify> does work, but that is the % one.

You can tell me what is that you are trying to do? maybe i can find a way around it over here.

i sent you a friend request so you can talk to me on private. :)