The only possible hindrance I can think of is that if you build something on .net but someone else manages to score the .com for that name then you may have fut

The only possible hindrance I can think of is that if you build something on .net but someone else manages to score the .com for that name then you may have future troubles. But since your company owns the both versions then that stands settled. Just out of curiosity, won't users be confused if you have 2 products for different fields sharing same names one on .com and another on .net?