If you sort by location (the same as in your Duplicate File Finder: Option - select by shortest path post) then you can influence whether the first FolderA or the first FolderB file is kept while the others are deleted.
If there are multiple duplicates of each file that you want to keep in FolderA then it's a bit more complicated:
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Do the duplicate find, and then close the utility panel so the lister goes back to normal mode, without checkboxes.
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Make sure nothing is selected to begin with.
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Use Edit -> Select by Pattern.
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(Click Advanced if it opens in simple mode.)
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Make sure the Action: drop-down is set to Select matching items.
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Set the filter to whatever you want. e.g. Location - Match -
*\FolderB(|\*)- Use wildcards -
Click OK and the files you want to delete should now be selected. Double-check that everything is as you want it, then delete them as you would normally.