Maybe or maybe not.

Is his Schedule C business affiliated with the partnership in any way?

If no, and the SEP Agreement was done properly, the SEP contribution can be based on the earned income from the partnership only and not include the Sch C loss.

In any partnership, the SEP contribution is based on the same percent of earned income for everyone. If your partners have Guaranteed Payments that are not even, when combined with Line 1 income, they will have different earned income upon which to compute the SEP contribution.