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I couldn't reproduce this issue.
Which version of WinMerge are you using?
Could you please attach a screenshot of the state just before copying the empty files?
It happens in both 2.16.34.0 and 2.16.36.0. It only happens using binary contents compare mode. All other modes work correctly.
Steps to reproduce:
Create two directories: "left" and "right"
In "left" directory, create a zero length file "empty1.txt", a file "test1.txt" containing "testing123", and a file "test2.txt" containing "testing123".
In "right" directory, create a zero length file "empty2.txt", a file "test1.txt" containing "testing456", and a file "test2.txt" containing "testing456".
Compare "left" directory to "right" directory using binary contents compare mode.
It correctly recognizes that the "test1.txt" and "test2.txt" files are different.
Select all files and use the "copy to right" or "copy to left" button on the toolbar.
The "Confirm Copy" dialog window says "Are you sure you want to copy 2 items?"
Clicking "yes" only copies the "test1.txt" and "test2.txt" files.
In folder mode, empty (zero length) files are not copied when they do not exist on the target side.
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