You are unlikely to be arrested and will not have a ban from entry if you have a D/S visa. However, you would not have been covered by cap gap is your OPT end date was before April 1; this may be the source of your company's reluctance to file.
To make yourself feel better, consult an attorney for an hour. He should also be able to tell you how best to present the situation if you go for US visa in the future.

