Note: I have verified that this affects 1.7.4.1 and 1.7.5.1.

To recreate this:

1. Upload sample1 to a project.
2. Create a new session resource under the sample1 session.
3. Upload the attached file to the newly created resource. Confirm that you want to extract the zip.
4. At this point, the resource should look like the attached screenshot.
5. Note the existence of both A/A.txt and NESTED/D/A.txt within the resource.
6. Download > Download Images.
7. Keep everything checked for download in column 2 on the download page.
8. Choose "Option 2: ZIP download", and check either/both of the "Include project/subject in file paths" boxes.
9. Initiate the download.
10. The zip downloads instantaneously. That's because:
    1. All of the study data is missing.
    2. There's only three files: A.txt, B.txt, C.txt. (One of the A.txt files has been lost)

Notes:

1. I have no idea why this only seems to happen if you check "Include project in file paths" or "Include subject in file paths" (or both).
2. Note that since the duplicate files are in separate directories, it shouldn't even be a problem in the downloaded zip. This is demonstrated by keeping both boxes unchecked for project/subject, and the download works just fine.
3. When this happens, this is logged:

   2019-02-07 23:52:12,612 [ERROR threadPoolExecutorFactoryBean-26] org.nrg.xnat.web.http.AsyncLifecycleMonitor.logLifecycleEvent():64 - An exception occurred during asynchronous processing. Request for task of type org.springframework.web.servlet.mvc.method.annotation.StreamingResponseBodyReturnValueHandler$StreamingResponseBodyTask: HTTP request to URI /xapi/archive/download/admin-20190207_235211/zip by user 'admin'

   java.util.zip.ZipException: duplicate entry: Sample_Patient/Sample_ID/TEST/A.txt

   at java.util.zip.ZipOutputStream.putNextEntry(ZipOutputStream.java:232)

   at org.nrg.xnat.web.http.AbstractZipStreamingResponseBody.writeTo(AbstractZipStreamingResponseBody.java:191)

   at org.springframework.web.servlet.mvc.method.annotation.StreamingResponseBodyReturnValueHandler$StreamingResponseBodyTask.call(StreamingResponseBodyReturnValueHandler.java:106)

   at org.springframework.web.servlet.mvc.method.annotation.StreamingResponseBodyReturnValueHandler$StreamingResponseBodyTask.call(StreamingResponseBodyReturnValueHandler.java:93)

   at org.springframework.web.context.request.async.WebAsyncManager$5.run(WebAsyncManager.java:332)

   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)

   at java.util.concurrent.FutureTask.run(FutureTask.java:266)

   at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)

   at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)

   at java.lang.Thread.run(Thread.java:748)