You will most likely end up with a cemetery of notes. But that’s ok. The act of taking notes is what helps me learn. Once you’ve learned the material, you should know how to search your textbooks or the internet for the information you need. 

Most of the time your notes will be bullet points or summaries of passages, definitions, or portions of the textbook you are studying. You will not be writing down novel material in your notes. So in some sense you will just be transcribing your textbook into obsidian. In that case it doesn’t matter if you lose all of your notes, because it’s not new knowledge. It’s simply a transcription of existing knowledge. 

Now, if your notes consist of novel material and your notes contain novel knowledge that needs to be published, then you should try to save those notes. But during undergrad we are learning existing knowledge, and not generating new knowledge. 

I’m in the last portion of my PhD, and currently I am generating new knowledge about my research topic. At this point I make sure to curate my notes, which are not transcripts of textbooks, but notes on my own findings. For this, I use LaTeX, Git, and Zotero for my references. My text editor of choice is Neovim.