Wolf, Bath,
You are absolutely correct. Torah and mitzvos are eternal. As the Rambam writes (I just learned this in shlosha prokim):
דבר ברור ומפורש בתורה שהיא מצוה עומדת לעולם ולעולמי עולמים אין לה לא שינוי כו’
Or, as he writes in Hilchos Megilla, that all of Nach (except Megilla) will be nullified in Yemos Hamoshiach, whereas Chumash and all the halachos will exist forever
הלכות של תורה שבעל פה שאינן בטלים לעולם
The problem is that the idea of mitzvos being nullified in Yemos Hamoshiach is not the imagination of some overzealous messianists based on some vague midrashim, rather clear gemoros with halachic implications (not aggada).
See Niddah 61b: מצוות בטלות לעתיד לבוא (regarding the halacha of בגד שאבד בו כלאים). See Tosfos there, and Rambam Hilchos Kilayim 10:25.
See שדי חמד כללים מ’ ס”ק ריח for more examples.
This seeming contradiction is something that Torah scholars have struggled with (though obviously in a respectful way. I am shocked by the audacity of Bath “Anyone who says otherwise, even chazal, is either wrong or a misunderstanding.” עפ”ל עפ”ל)
Among others, Rav Elchanan Wasserman discusses this at length in Kovetz Shiurim (ח”ב סי’ ט) and proposes two answers.
The Lubavitchers Rebbe as well has a brilliant pilpul on this sugya. See here: https://www.hebrewbooks.org/pdfpager.aspx?req=59257&st=&pgnum=206
Chas v’shalom to dismiss the words of chachamim. If we don’t understand, we must ask and learn.