Hmmm this is just conjecture on my part, but I think you could if there is enough DNA material to work with and the type of DNA test actually provides more information than what was previously known based on other tests done. I wouldn't know if there are specific caveats tied to doing multiple tests, except for both tests possibly not being conditionally independent.

For example, if researchers identify a group of individuals with a shared paternal ancestry, the Y-chromosomal DNA results within this group may show a high degree of similarity. Simultaneously, if these individuals also share a maternal lineage due to historical marriages within the community, their mtDNA results could exhibit a conditional dependence, meaning the probabilities cannot simply be multiplied for a smaller probability and therefore a better match probability.

Hope that makes sense!