What's the affect of having a root canal while being pregnant unknowingly?

No big concern: Root canal therapy (rct) is not contraindicated for pregnant patients. However, there are a lot of steps in rct. Some obgyn do not want pregnant patient to have epinephrene which is commonly in local anesthesia. Some irrigants used in rct might have certain chemicals that are controversal in pregnacy. If you already got it done and have no problem, you should be ok. Just let your obgyn know.

Rct and pregnancy: There is a greater risk in allowing an infected tooth to continue during the pregnancy.