It takes about 4-8 weeks (it may be sooner) for the IRS to process a tax return that was filed without an 8962/1095-A. If the delay is causing you a hardship then contact the Taxpayer Advocate Services for more help. http://www.taxpayeradvocate.irs.gov/contact-us
Your refund amount may go up or down depending on your income and the amount of Advanced Premium Tax Credit you received on the 1095-A.
The change is calculated on Form 8962. If you have an amount on line # 26, that amount will be added to your refund. If you have an amount on line # 29 instead, this amount will be deducted from your refund.