FIFO logic run during TO creation once TO creation is done there is no impact however it is standard practice that before making any config change make sure that there is no any open document exist in the system related to that config.
I see hundreds of open transfer orders and transfer requirement in the system and now they are asking of removing this WM FIFO Picking Strategy.-----Iam wondering how come you have more then 100 open transfer order / TR in the warehouse I have never seen a warehouse where more then 100 transfer order exist and waiting for processing as it is a continuous activity and TR needs to be converted in TO and TO needs to be processed. Also what is the reason for changing the strategy what other strategy are you planning to use instead FIFO