Shu could have possibly asked Free to help with Lean. Free may have went to New York during this travel and met Shu. Which means after Free got Fafnir repaired, Free could have been traveling around the world and training along the way. It's possible that in a flashback in Beyblade Burst Rise that Free may have repaired Geist Fafnir. Free may have had Fafnir or had it before Phi destroyed Fafnir. This most likely that Free got Geist Fafnir repaired after Phi destroyed Fafnir in Beyblade Burst Turbo. This could possibly mean that Free couldn't have repaired Geist Fafnir after Beyblade Burst Turbo. That could mean that Free had another Fafnir that's been destroyed.
Free could have use the first Fafnir that he owned.