The GDPR is effectively irrelevant here unless your goal is to host Perkeep as a service. Yes, if you upload your own personal database to Dropbox then Dropbox does still have GDPR obligations to you but those obligations do not extend to managing your files for you also, as an analogy if you were to upload a zip file to Dropbox it would not be reasonable to expect them to remove a file from within that zip file at your request.