From the rules (emphasis mine):
Replace three Resources
Three times in a row, take any resource of another player from the game board and place it on any empty field on any trade route in the same country (i.e., you may not move a resource e.g. from Wales to England))
Replace two Resources
Relocate any two resources, no matter to whom they belong. Resources may not change the country they stay in (e.g., re-source in Wales remains in Wales). Unlike „Re-place three Resources“, exchanging two resources is possible
The phrases 'from the game board' and 'any two resources' seems very specific and consistent with each other. Does this mean that you can move resources from cities, as well as resources from trade routes? Perhaps Kontors are not considered to be 'resources' (traders & merchants)?