I see that HipChat offerrs this functionality, but can't find any mention of Slack in Flowdock help...
Importing chat history from Slack - Atlassian Documentation
Hi Tim! Thank you for your question. At this time we do not have this functionality, however, if you would like, I would recommend visiting www.flowdock.uservoice.com and submitting a feature request. Our Product Owner will review and prioritize the feature requests for consideration from there.
Apologies for not having a solution to provide at this time.
Thank you again!
Kind Regards,Hilary Flygare
FR posted here: Import chat history / Migrate from Slack – Customer Feedback for Flowdock