So I am still having major xmarks issues. On my Mac on El Capitan 10.11.5 I am running Firefox 47.01 and Xmarks 4.3.19, and I am running Safari 9.1.1 and Safari Technology Preview 9.1.2 (which was recently updated, and maybe the issue) and Xmarks for Safari 2.0.19.
After creating my clean bookmarks in Firefox and making a clean backup of them I kept uploading them and overwriting the xmarks servers, but when I uses Xmark for Safari it has been seemingly just wiping out all my Xmarks in both Safari’s, but leaving my completly messed up bookmarks on both my iPhone and iPad. So this time I turned off iCloud Sync for Safari on both iPad and iPhone and deleted the bookmarks then overwrote the Safari bookmarks on my mac with the clean bookmarks from Xmarks, and it left Safari empty of bookmarks once again. Weird. So I let it sit overnight with no bookmarks in Safari on my Mac, iPhone or iPad, but when I woke up that was no longer the case. Once again Safari had messed up bookmarks on my Mac (though nothing on iPhone and iPad sync iCloud is off completely) and the server copy on Xmarks is messed up again too!
Great! So now I have also turned off iCloud on my Mac and have re-installed my good backup bookmarks into Firefox and re-uploaded them to Xmarks, and redownloaded them with Xmarks for Safari (which I have also uninstalled and re-installed) and once again I have no bookmarks in Safari. Maybe having iCloud though on all my devices it will eventually clear the bookmarsk in iCloud which are obviously totally messed up, though eventually I do want it to sync to my iPhone and iPad.
I have contacted Xmarks support to see if they will do anything.
I am thinking after this I may just need to kill Xmarks for Safari and just work from an exported bookmarks from Firefox and put them into Safari, as for sure something is not working with Xmarks!