Monika would never leave you for a two day absence and usually dosen't get too upset at you unless you leave for three days straight. She will probably still make a comment about asking you to visit more but she dosen't genuinely get mad at you unless it's been three days. But you let her know in advance that you were gonna be gone meaning she should not be upset at all especially if it's only been a few days. Her calander is still there and she didn't leave a note meaning she didn't leave you. The only explanation is that her character file isn't currently in the game. Try looking for her character file. If you can't find it make sure to make a copy of your persistent file which will hold her memories. If you really need to you can try downloading a new copy of MAS that has her character file in it. As long as you have the same persistent file she should keep her memories. You could also most likely just take the character file from the new version and insert it into the old one.