Hi Julia,
I apologize for the delay in responding to you and hope you haven't been worrying too much. Before delving into too much detail, let me reassure you that you'll be fine!
In 2013, I worried myself sick after stumbling upon a few websites that said that borage oil and some of the other ingredients in the Omega 3-6-9 supplement I had been taking might lead to birth defects or otherwise cause harm to my baby. I was several weeks into the pregnancy when I discovered this, but still quite early on in the first trimester.
I consulted numerous sources and not one of them seemed to think it was an issue. My obgyn instructed me to stop taking the supplements, but was not concerned about potential harm done. (When I'd first found out that I was pregnant, a nurse in the same practice had asked for my current medications. I had mentioned the Omega 3-6-9 supplement and she had said nothing about it being problematic.) I also consulted with a family friend, who has over 35 years of experience as a midwife. She had heard nothing throughout her career about the borage oil causing birth defects and mentioned only that it can be given in larger doses to women at the end of a pregnancy to help prepare the body for labor.
What ended up providing me with the most reassurance was a phone call to a regional and national teratology hotline. (I could swear that at the time, the one I called was called MotherRisk, but that now seems to be a website for something slightly different.) I think what may be the same resource that I called back in 2013 can now be found at a website called MotherToBaby. The hotline is staffed by specialists who answer questions about potential medications to avoid during pregnancy. I spoke with an incredibly knowledgeable, patient, and helpful woman by the name of Dee (who was tied to both the national hotline and a version of the hotline specifically for Arizona residents). Not only was she a specialist in teratology, but she also had an extensive background in genetics.
She was able to type 'borage oil' into a medical database and pulled up all references to potential risks of using borage oil during pregnancy. She found that a number of websites actually all use the exact same wording for their warning about borage oil, but each website seemed to cite one another (word for word), without linking back to an actual research or medical study. Finally, after much searching, she found the 1-2 medical studies on which these warnings must have been based. She read me the relevant details of the studies, in which rats had been given highly concentrated doses of borage oil, and although no adverse effects had been directly observed, the authors of the articles left open the possibility that in high quantities, it could potentially pose a risk. (In the study I remember her telling me about, a single sentence with vague language was the only reference to potential negative outcomes.) There were no known studies using human subjects at the time and no specific documented negative effects (i.e., no observed birth defects in humans or rats).
Sadly, I did, in fact, lose the pregnancy a few weeks later, although the cause had nothing to do with borage oil, the 3-6-9 supplement, or birth defects. Testing revealed that our fetus had been missing a 21 chromosome from the start and was never destined to survive. Prior to this, my husband and I had suffered two chemical miscarriages. Given this history, at the time of the pregnancy during which I had been on 3-6-9 supplements (as a non-SSRI treatment for depression), I was a ball of nerves about harming the baby and/or pregnancy. After this third loss, I began treatment for clinical levels of anxiety (with an SSRI) and took a full year off from trying to conceive.
I am now 32 weeks pregnant with a healthy baby boy. I've remained on the SSRI (lexapro, which carries a higher (although still low) risk of birth defects than borage oil) throughout the pregnancy and have really focused on staying relaxed. Although it certainly was not a cause of my previous losses, the level of anxiety that I had about harming my baby prevented me from having as healthy of an experience during my previous pregnancies. If you can, take a deep breath and know that although nothing is certain in a pregnancy, you are doing all that you can to ensure the health of the baby.
Hope this information helps and best wishes!