The FLP/FRT system permits rapid phenotypic screening of homozygous lethal mutations in the context of a viable mosaic fly. Combining this system with ovo^D dominant female-sterile transgenes enables efficient production of embryos derived from mutant germline clones lacking maternal contribution from a gene of interest. Two distinct sets of FRT chromosomes, carrying either the mini-white (w ^{+ mW.hs} ), or rosy (ry⁺ ) and neomycin (neo^R ) transgenes are in common use. Parallel ovo^D lines were developed using w ^{+ mW.hs} FRT insertions on the X and chromosomes 2R and 3L, as well as ry⁺ , neo^R FRT insertions on 2L and 3R. Consequently, mutations isolated on the X, 2R and 3L chromosomes in a ry⁺ , neo^R FRT background, are not amenable to germline clonal analysis without labor-intensive recombination onto chromosome arms containing a w ^{+ mW.hs} FRT. Here we report the creation of a new ovo^D line for the ry⁺ , neo^R FRT insertion at position FRT42D on chromosome 2R, through induced recombination in males. To establish the developmental relevance of this reagent we characterized the maternal-effect phenotypes of novel brother of tout-velu alleles generated on an FRT42D chromosome in a somatic mosaic screen. We find that an apparent null mutation that causes severe defects in somatic tissues has a much milder effect on embryonic patterning, emphasizing the necessity of analyzing mutant phenotypes at multiple developmental stages.