Did BSc, doing MSc, applying for PhD. Is it frowned upon to not have a letter from my BSc advisor? I am currently pursuing an MSc and am preparing my PhD application. For this reason, I reach out to professors I know well in order to ask them whether they would be willing to write recommendation letters for me. I got a BSc from a different university and I obtained it by writing a final thesis.
My question is:
At the time of the application, I will only have written a BSc thesis and not yet the one for the MSc. Would it be considered a &quot;red flag&quot; if the professor who supervised my BSc thesis is not one of the three references I provide with my application?
The reasons why I hesitate to ask that professor is that even though my thesis turned out fine, I entirely interacted with one of her PhD students during the process of completing it and not with her personally (there are other professors who I know personally). Also, because she teaches at my old university and not at the one I am currently studying at, I question whether she might have lower incentives to positively recommend me.
Related: here
Will you get a recommendation letter from your current (MSc) supervisor? I would assume that would be the most relevant and important one. References from your last position will likely be the most relevant for the next one, as those are the people that have worked with you most recently. 

It might be a bit curious that you omit a recommendation letter from the only completed work you have by the time of application, however if the references you attach to your application are more relevant in terms of timing and topic I think it wouldn't hurt your chances.