Sorry for not being clear, Matt. You shouldn't need to copy all the jars into both module's lib directories as both directories' jar files should be on the classpath. Each module's deployed lib directory should contain its own jar file(s) (e.g., compBioStudy-17.2.jar) as well as the jar files of the module's external dependencies.

The Gradle build should be putting all deployed jars into the same place the ant build did, and once the jars are in place the build system's job is done. It shouldn't affect the running server, unless it has put the jar files in a bad place.

Here are a couple of things to try:
- Use 'jar tf' (or something similar that will show you the contents of the jar file) to confirm that 'org.labkey.compbiostudy.dataLayer.baseClasses.DBHelper' is actually in the jar file in the build/deploy/modules/<first module> directory
- If you have a deployment created from your 17.1 LabKey, compare the build/deploy/modules/<first module> and build/deploy/modules/<second module> directories from that deployment with the one from 17.2

Let us know what that reveals, if anything.

Susan