Without any adjustments, Railway Empire’s economic system of each scenario is stable. If changes to the parameters of the *.ini files are made, it could come to an imbalance of the economic system, which might lead to undesirable effects like uncontrolled growth or decline of a city, advantage or disadvantage of a player and the game’s experience might suffer from those effects.
Caution: While modding, it might be a good idea to create backups on a regular basis. That way, you can go back to a previous version in case of an “accident”. To create a backup, we would recommend to copy the (Tiled) *.tmx file and the (Tome) *.tproj file from your scenario to a different directory, so it will be able in case of an emergency.
Moving cities or rural businesses will most likely result in ugly clipping or similar issues, eventhough it should not have an impact on the game from a technical point of view. Anyway, reverting the data might be an option for those cases, too.