Hello (this is for amusement only - an interesting experience), if anyone would like to know why the idea with experimental branch of minimals didn't work out in its current form (I wanted to have a full tree and a separated tree with fixes only, but it took files from current and experimental in an arbitrary order). This is an answer from the mailing list: ------ Duh. I realize now that it's perfectly reasonable for you to be able to reproduce the problem while I can't. Versions 2.6.9 and earlier of rsync sort the file-list using the C library's quicksort, an unstable sort, so the results in case of duplicate files are highly sensitive to both the C library implementation and the order of directory entries in the source (which in turn is sensitive to the filesystem implementation). You probably have both a different C library and a different filesystem than I do. In any case, since rsync 3.0.0pre1, the default file-list sorting algorithm is a mergesort, which is stable, so files from earlier source arguments take priority. If you upgrade to an rsync 3.0.0pre* version, your scenario should work consistently. If it doesn't, that's a bug we should try to fix.