The associated spreadsheet file contains new or corrected data for 42 EY lines that both FlyBase and GDP databases categorize as having only a single insertion. The type of data that has been added/changed varies among the lines. I have attempted to categorize this in column C. The first spreadsheet (labeled All) has all of the lines and the others have subsets with different types of added/changed data. These subsets are not mutually exclusive, since some lines have several types of new data. I have tried to use a yellow fill for cells with added/changed data on the first (All) spreadsheet.
Most of the corrections in genomic sequence location are minor (< 100 bp). EY01559 is an exception. The FlyBase location data for this line are contradictory. The symbol is P{EPgy2}miltEY01559, but the FlyBase chromosomal and sequence location are for a site on a different chromosome (3L) than the milt gene (2L). I think that there must have originally been two insertions, one on 2L and one on 3L. I haven't thoroughly investigated the history, but I think that the iPCR done before balancing detected only the 3L site and the iPCR done after balancing detected either only the 2L insertion or both the 2L and 3L insertions. I separated the 2L insertion (in milt) genetically and balanced it; I was unable to recover the 3L insertion. You may want to annotate this as two insertions, but with the current BDSC stock having only the 2L insertion in milt.
There is a change in the gene-allele assignment of EY04120 that deserves further explanation. There is a personal communication from me that gives the release 3 coordinate of the EY04120 insertion site, but FlyBase has no entry for the release 6 sequence location. The P-element in this line is inserted in a copy of TE 1360 that can be mapped to a site in the sequenced reference genome at location  3R:5822494  (release 6), although there is no copy of TE1360 at this site in the reference genome strain. This is ~ 1 kb upstream of the Hpr-1 gene (CG2031) and FlyBase has EY04120 annotated as an allele of Hpr-1. However, the current gene annotations place this site within the 3' UTR of one transcript of the CG2023 gene. It's especially hard to speculate on the gene(s) affected by EY04120 because it is inserted in a polymorphic TE 1360.