Interesting question.
Compass and Mesaba as of today are no longer "affiliates".
It appears the flows are now "negotiable" again. Its up to management and ALPA whether to continue.
The default position for Mesaba seems to be that the flows terminate. Compass is less clear except that their management can unilaterally terminate the flow if they wish. I would expect them to terminate it. Its nothing but a training cost for them.

Here's the Mesaba language:

A. General
1. The Flow through rights established in this Letter of Agreement shall be subject to the following limitations:
a. The right of any company pilot to Flow Down to MSA, or MSA pilot to Flow Up to NWA, pursuant to the terms of this Letter of Agreement, shall not become effective prior to January 1, 2008;
b. The right of any company pilot to Flow Down to MSA, or MSA pilot to Flow Up to NWA, pursuant to the terms of this Letter of Agreement, shall be effective only so long as MSA remains an Affiliate of the Company, provided the parties will, prior to the termination of the Flow through rights referenced herein, meet and confer for the purpose of discussing whether continuation or modification of this Flow Through Agreement would be appropriate given the circumstances at that time. Any continuation or modification shall require the mutual agreement of the parties.

Here's the Compass language:

A. General.
1. This Letter of Agreement governs employment opportunities at the company and at the Feeder Carrier Affiliate for all NWA pilots with a system seniority number together with future pilots employed by the Company and pilots employed by the Feeder Carrier Affiliate. In the event of a sale of Feeder Carrier Affiliate such that it is no longer an affiliate of NWA, the flow up rights of Feeder Carrier Affiliate new hire pilots (Sections D and H below) can be terminated by the Feeder Carrier without impacting the Company’s upper cap in Section 1.B.7.c. (e.g. upper cap of 90)