You should be able to accomplish that in Abbyy Finereader itself, procedure might vary depending on its version.
https://help.abbyy.com/en-us/finereader_sprint/12/crop
under "+ cropping pages ..." hyperlink
https://help.abbyy.com/en-us/finerea...nagingpdfpages
There is also a pdf-cropping thread here
https://www.mobileread.com/forums/sh...ad.php?t=83053
Besides an already mentioned k2pdfopt I've been using Briss too.
https://www.youtube.com/results?search_query=briss+pdf
https://github.com/mbaeuerle/Briss-2.0
If you have not been using Koreader app on your Kobo Aura One, you should install it, because of its various pdf margin cropping capabilities and reading modes, including k2pdfopt's reflow mode for the scans.