Answer
Run a clean build before troubleshooting further — in the Source folder of the Build Home, RMB and open a command prompt there, then run _msbuild.cmd clean (or _ant_compile.cmd clean if the affected build is the Ant build instead). After the clean completes, a log file is created in the Build Home folder — check that its date/time actually updated to confirm the clean genuinely ran — then rebuild normally. A clean build clears out whatever stale intermediate state was causing the .dll files to not refresh.