As a small population (founder or remnant) a self-incompatible species might fare poorly since it might by chance contain only individuals genetically identical for the self-incompatibility alleles, leading to very low levels of reproduction. However, if unlike individuals did remain in the small population, higher genetic diversity, important for adapting to changed conditions, would likely be found than if the small population were from a self-fertile species. The self-fertile species would, however, have a much easier time reproducing even from a very small number of individuals.
Work Step by Step
The key to this answer is to see the balance between ease of reproduction (self-fertile) and maintained genetic diversity (important for evolutionary survival) for these two scenarios.