I have done this on my Fenix 5 shortly after getting it and it behaved in the same way that my Fenix 3 did; so yes the files are rebuilt if you format the drive. That said, I have only ever needed to do this in conjunction with a full button combination master/factory reset.
(All of the above said, I would not recommend routinely doing this. The various reset methods are best tried first, if you are seeking to clear an problem; this probably should be treated as a last resort)
