During migration MNE tool checks messages on the folder level, not on the mail store level. Practically, if the message was migrated from the Folder A on the Source to the Folder A on the Target during the first migration, during the re-migration process it will compare the messages from the Folder A on the Source against the messages in the Folder A on the target. If the message is in the Folder A on the Target, it will not migrate the message. If the message was moved to i.e. Folder B on the Target, the MNE tool will not check the Folder B and will re-migrate the message to the Folder A on the Target. This will practically create a duplicated message.
If the message was deleted on the target, the MNE tool won’t recognize this action and will again re-migrate the same message.
Office 365: Auto-Expanding Archives - Explained
What are auto-expanding archives?
It's Microsoft O365 ability to grow mailbox archive over the normal 100GB limit.
When can I expect the archive to expand?
Essentially it's called transition threshold and provisioning of auxiliary archives will start when this value has reached 90GB.
How much content is being moved to auxiliary archives during the transition?
This value may change but at the moment it's around 50% of the occupied size in the main archive. Practically, if you have 100GB in the Main archive, when the process kicks in it will move about 50GB into the auxiliary archive.
How is the transition size calculated?
Occupied space is essentially any folder in the main archive that is movable or type DeletedItems or RecoverableItems. DeletedItems and RecoverableItems folder types are not movable and for these folders the process creates movable folders under the root of the folders and move the content to those newly created folders to get picked up by managed folder assistant. Folders that do not fall into those categories are not taken into consideration during expansion.
Can I ingest more than 100GB into the archive via a third party tool (i.e. MNE)?
Microsoft doesn’t officially support bulk ingestion of more than 100GB into the archive at any one given time. There is currently work on going to provide solutions for these scenarios in the future, but they don’t have any timelines to share right now. Since there are multiple ingestion scenarios we suggest that you contact Microsoft so that they can understand your situation and advise you on the best way forward for your ingestion project.
For more information please refer to Microsoft and below website link
https://techcommunity.microsoft.com/t5/exchange-team-blog/office-365-auto-expanding-archives-faq/ba-p/607784
Feasible workaround
The PST Export/Import process is still a viable solution. If you are fortunate enough to have a small number of mailboxes, this may not be as painful as if you had a large number. Otherwise, for a large mailbox you would need to break the mailbox apart by exporting it into multiple (e.g. up to) 20BG PST files. Using the Network Upload from the Security & Compliance Center you would then need to upload the PST’s for ingestion to Exchange Online mailbox