It shouldn’t affect any running interfaces, but it might mess up your alerts. I seem to remember having alerts that were based on last message time firing unexpectedly because of this.
If you only want to reset the amount of msgs/bytes then hcimsiutil -X is an option. As per the manual: Keep times but zero ALL other thread section data.
Zuyderland Medisch Centrum; Heerlen/Sittard; The Netherlands