FPGA pin multiple usage

Hi all,
i use 10 fpga pins towards a connector on my board. They are set-up as 5 
inputs and 5 outputs. on this connector i can have multiple little 
boards and their function changes .

now for my question, is it good or bad practice to vhdl condition the 
routing to these pins?

for example out pin10 is used as 1ms pulse for zeroing board1.
can i use out pin10 for uart TX for board2?

the little boards are not replaced 'live'. meaning that once the fpga 
powers-up,
it will identify the board connected and set appropriate routing that 
will not change (at least not until another power toggle).

thank you in advance
sparkyT