How can my company file PERM for me while I am on EB-5 with my I-829 petition pending?

As long as your I-829 is pending, you should be able to continue on your conditional green card obtained through your I-526. Therefore, you should not need to pursue a green card through EB-2. However, there is nothing that prevents you from seeking a green card through two avenues at the same time in this case either EB-2 or EB-5. The only rule though is that in the event that either avenue results in a green card, the other pending application would be canceled by the USCIS. Thus, you should consider the amount of time and money that you would expend on both EB-2 and EB-5 processes as you pursue both at the same time. Could you get in touch with an attorney to review all your options?

They can start the PERM but you may need to consular process at the final stage if not in a nonimmigrant status.

I am not certain why you think the I-829 could be denied, but if your company wants to do a PERM case for you, you do not have to wait for the H-1B first then start. Please note the PERM process takes almost 2 years because the request for the prevailing wage takes almost a year to obtain before your employer could even do the local recruitment to show they cannot find U.S. workers for your position. Also, all the cost for the Dept. Of Labor PERM process, including advertising cost and the attorney fee must be paid by the employer.

You are already a conditional green card holder - you will not be able to obtain a green card through the PERM process unless you abandon your current I-829 process.