Aligning files with name name in subfolders

[MixAndMatch]

I am running Version 4.2.7 (build 23479), 64 bit edition on Windows 10.

I am having an issue where I am unable to align a file on the left side to a file on the right if there is another file with the same name in a subfolder (and flatten mode is on).

For example:

Left Side:
1.txt

Right Side:
1.txt
sub/1.txt

Beyond Compare seems to align the left 1.txt with sub/1.txt on the right and I am unable to change this even when right clicking and using "Align With". I have attached an example. If the files on the right have different names, alignment appears to work as expected.

[Chris]

Thank you for reporting the problem. There isn't a workaround to make Align With work with duplicate filenames and Ignore Folder Structure. Making Align With work in this scenario is on the feature request list for a future version of Beyond Compare.