Anton, I pushed a fix https://bitbucket.org/petsc/petsc/commits/28865de08051eb99557d70672c208e14da23c8b1 in branch hzhang/fix-superlu_dist-reuse-factornumeric. Can you give it a try to see if it works? I do not have an example which produces your problem.
In your email, you asked "Setting Options.Fact = DOFACT for all factorizations is currently impossible via PETSc interface. The user is expected to choose some kind of reuse model. If you could add it, I (and other users probably too) would really appreciate that." We do not allow user set superlu' Options.Fact = DOFACT. If user changes matrix structure, then user must call KSPSetOperators() -> call symbolic matrix factorization again, in which we set Options.Fact = DOFACT. Hong
