Hello Manu,
this should not affect a system upgrade, since the objects used by SFW5 to turn on the BF already existed beforehand. Some of them, of course, now are active. Some enhancements and business set were created but this will not affect the upgrade.
However you should take care about the change requests created on this system and that might include objects from this BF. If you transport it to your next system on the landscape which does not have this BF active you might face errors, since objects will be inactive.
Best regards,
Tomas Black