HI,
Sounds like this "import external" node is a custom node developed for your organisation, so you will need to check with your internal support team as to how it works. But in general the way that MA runs its queries against the database is that there is a "primary" table for each subject level, and this table must contain the entire universe of subject_ids (for you it seems that means MSISDNs). Each query from a campaign always joins to this primary table. So if you load a another table with an MSISDN that isn't in the primary table, it will get dropped.
Regards
James