Thanks for your report.

I was able to reproduce the problem. I'll look into it.

Issue 2370 – Files modified by local custom command are not always uploaded to the correct remote directory

This is my workflow for uploading changed files to a remote server. I use Synchronize to compare the files and subdirectories in the local and remote, when the Synchronization checklist appears I select an individual file and run a custom command on it to see the differences in WinMerge:

This downloads the remote file to a temporary location to do the comparison. In WinMerge I copy across specific lines of code from local to the temp file, save and close. The temp file gets saved back to the remote.

The problem, if the changed file was in a subdirectory relative to the Synchronize, the temp file will get saved back to the upper level directory and not in the subdirectory. How can I fix this?

In Storage preferences I have the option "Append remote path to temporary path" turned on. However the temporary file is being created in the root of the temporary directory. Could this be the cause?