You could.... if you're transferring the same amounts of the sale, that's going to look bad, and odds are you'll have the paypal accounts linked as one owner.
To answer your post question, no paypal will not limit you if you have sales outside of ebay.
Be really careful. If the accounts have zipcodes that are near each other, paypal will not like it all and will come down on both accounts. You must be in different areas and must send invoices to self. I have tried this method before and after 2 shots it usually took both accounts down. Not the best way to do this.
If my paypal does not recieve ebay auction payments, will it get limited? 
