Hello and Welcome to Justanswer,
My name is XXXXX XXXXX I am here to try and assist your with your question.
I have enclosed door panel removal instructions, once you have it off you will be able to see what has let loose. It likely just a mater of reinstalling the bolt.
Do I need to worry about re-aligning the window, or is there a pre-set adjustment, or should I just have the window in the fully up position? Thank you!