Hi Pedro,
would you share with us your enviroment: Gigabytes to transfer, type of storage (dataferry-store and destination server), type of filesystem (maybe network filesystem?)... so maybe we could suggest some tips for your case.
In my humble opinion, the lost of deleted items information during the incremental migration should not have a major impact on migration itself, but obviously it depends on what you mean by a long time.

D0s0n