Yesterday I lost two items while transferring from my warlock to my hunter (299 Mida Multi Tool, and 292 Hoosegow?). They were both duplicates, meaning I had one in each class of player. I was simply trying to infuse the duplicates and just share each item between classes. Not sure there is anything I can do now? I assume the issue is probably due to them being duplicate items as I have had no issues transferring gear between my classes that were not duplicates.
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Items that are "lost" while transferring via the companion app will normally be redirected to your vault. Check there.