The Merge folder comparison window enables you to review and merge the changes within different versions of a text file by launching file comparisons for each row of files that interests you.
To view the changes to a file, first select the file by clicking on it in the results list. Next, click the Launch File Comparisons For Selection 
button in the toolbar. A file comparison window will open and you can review and reconcile the changes between the versions
of the file.
Launching multiple file comparisons
You can open file comparison windows for more than one file at a time by selecting multiple files in the folder comparison
results list before choosing the Launch File Comparisons For Selection button. Hold down Cmd or Shift when clicking on files in the folder comparison windows to select multiple files.
You can also use the Select Changed 
button in the toolbar to select all the changed files before clicking on the Launch File Comparisons For Selection toolbar button.
Limiting the number of opened file comparisons
To avoid an overwhelming number of windows being opened at a time, there is a configurable limit on the number of file comparison windows that the folder comparison window will open. This limit can be adjusted using the controls in the Launch page in the Options dialog.
A typical method of working is as follows:
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Click Select Changed to select all the files that have changed between the first and second folder hierarchies.
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Click Launch File Comparisons For Selection to open a file comparison window for each of the selected files. A file is deselected when a file comparison window is opened
for it.
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Review and/or edit the content of the file comparison windows that were opened. Close each file comparison window when you have finished with it.
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Return to the folder comparison window when you have closed all the file comparison windows.
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Click Launch File Comparisons For Selection again. If there are any remaining selected files in the list, another batch of file comparison windows will be opened.
Repeat the last three steps until there are no more selected files.
Updating the folder comparison after editing files
To update the folder comparison after making changes to a file, select the file and choose the Re-Test Selected Rows command from the Edit menu to refresh the folder comparison results for that file after making changes.