Are you certain that you filled in the water definition tag block properly? Compare it to something like coagulation. The shader should be fine since they render fine for me on coag.
I've looked at the name of the shader you are using for the glass and is it fair for me to say you're using
tags\scenarios\shaders\human\military\glass\glass_interior.shader
If so that has a material_name of brittle_glass_for_unbreakable and with that I've managed to recreate your issue. You want to change that to something like brittle_glass for it to break properly.
If it's simple enough I just select the faces I want to separate and press CTRL+P to make them a separate object. Otherwise I use the knife tool.
Now about the file you have here, I see why you have the issue with the triangles out of BSP error. You have a cube for water but the material you assigned it has the shader symbols "?" and "!"
? Is a shader symbol that is for a two sided transparent material. That means that the mesh uses a transparent type shader and is made two sided. So lets say you have a plane that you wanted to be water. In order to make this plane render when you look at it from top or bottom you would use the shader symbol "?" along with "!" to make sure it has no collision. In short the ? Is for transparent shaders and duplicates the mesh and flips the normals. The problem here is that it is duplicated the mesh and that mesh is technically outside the BSP because of how the level is set up. This would not give you an error if it was instance geo but since it is part of the BSP mesh you can't have it set up like this. I've made some small modifications to the level you uploaded. Go ahead and examine it to see things you need. This should solve
1. The glass mesh not getting deleted after breaking - solution is to change the material name of the shader for it.
2. Objects getting displaced after compiling the level - Solution is to apply both scale and rotation to all objects in your level.
3. Triangles outside of BSP error from water mesh - Solution is to make the water mesh in a single plane and let the ? shader symbol take care of the rest.
You can read more on Blender map making here
https://pastebin.com/12Zb8Wiy
https://pastebin.com/TFCfEZCF
It covers basic level importing and instance geometry importing. They are currently only in english and haven't been updated for the latest Blender release but most of the differences are UI and hotkey related only. I'll update it for 2.8 and possibly have it translated to other languages like French in this case. Need to find someone who does both English and French for that last part tho