The code here keeps an AutoGetCollection acquired unnecessarily long:

https://github.com/10gen/mongo/blob/ed405958353e2d940fd23e4488cc4af722f168c3/src/mongo/db/modules/enterprise/src/magic_restore/magic_restore.cpp#L715-L735

We should ideally release the AutoGet as soon as possible to avoid having locks on two collections at the same time since it otherwise triggers a lock dependency inversion that SERVER-99150 detects (config -> admin database).