The biggest theories I’ve seen so far:

• Maethrillian survived the ancient war but fell apart in the intervening years leading up to the modern age due to a lack of care.
• Maethrillian remained intact up until the modern age under the care of surviving sentinels and is drifting somewhere waiting to be discovered again.
• Maethrillian was destroyed during Mendi B’s second coming. An extension of this theory proposes the Forerunners attempted to save the Mysterium before Mendi B returned and is the crashed ship under the Babd Catha Ice Shelf.
• Maethrillian was successfully moved whole out of the galaxy like the Lesser Ark before Mendi B could attack it again.