It sounds like she struggling with a lot of stressors right now. This could be the end of a relationship or more likely just a temporary phase where she has exceptionally high stress. Circumstances like this can try a relationship but is not fatal. I would talk this out with her and tell her that you need to be able to support her but she needs to lean on you somewhat so that the relationship is not strained. You can be a source of support for her but she right now has to be open and honest. Encourage her to not withdraw from you and use this as a way to get closer. You may have to take on some of the grief but the relationship will be stronger for it. Try to work out boundaries for your relationship including these new stressors. For instance how often will you talk during the day, what will she do when she needs your support, and how will you function as a couple.
See is she benefits those good night texts. Maybe that would make her feel happy at night when she needs it the most. As you lay out new boundaries you will learn to withstand stress as a couple. Have this discussion as soon as possible
Then you have a choice to accept what she is saying as face value or not. She is saying there is no problem. You have to take the initiative to share your concerns with her - specifically why you are having doubts. You have to talk about stress and alternatives ways to deal with it that won't damage the relationship. Let her know what your expectations are and how you feel when she stays away. You may very well see a future. That is why it is important to cover this with her now. If you have a future together then there may be others events that put a strain on you both. Handle this one now so the next time there isn't this unhappiness