I would worry about JAL canceling your route more than them not honoring a partner airlines award. An issued ticket should be honored no matter which alliance JAL belongs to. The only difference should be you lose your OW elite benefits if JAL has switched alliance by the time you fly, i.e. priority check in, boarding, baggage, lounge access, etc.

And who knows, BA might remain as JAL's partner even if JAL switches to Skyteam (JAL is a partner of AF right now). But if you are really worry about it, you can wait till Jan 20. Supposing ETIC will make a decision by that date and it will be clearer about JAL restructuring plan by then.