After discussing with Josh and others, I merged the folders of customModules/EHR_reporting (a file based module) into customModules/ehr/, which contains a java module. None of the folders overlapped, so this basically involved moving the views, queries, reports and web folders.

After doing this, queries and reports are working fine.

The problem is that I am not able to access HTML views or JS files. The old address for a page is something like:
http://localhost:8080/labkey/EHR_Reporting/WNPRC/EHR/animalHistory.view?

i modified it to:
http://localhost:8080/labkey/ehr/WNPRC/EHR/animalHistory.view?

to reflect the new location. however, i keep getting a "404: page not found" error. this should be all that's required, right? is there some odd thing going on b/c EHR is java-based?

I did notice that in the following location was created on my HD, which is empty:
<labkey root>\build\deploy\modules\ehr\web

could the java module be creating this empty location, which is overriding the file-based module files?

thanks for the help.