The OS will not be affected, TWRP (or other recovery programs) reside in the recovery partition, separate from the OS.
Backing up your important data beforehand anyway is always a good idea 
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Latest TWRP and instructions: Fairphone 2
Because most people want to have Fairphone OS, and you can easily install Fairphone Open OS yourself.
Old info, ok … And sure, theoretically there could be other ways … and they could end up in a commercial or at least logistical nightmare for such small company.