At no point do we remove your mod archives so the worst thing that can happen is the conversion process fails and you're left with an NMM that contains all your previously downloaded files but with none of them active or installed.
As we're as yet unsure how successful the conversion method will be we're recommending people backup their current NMM installations before attempting to upgrade. Script installers will have to be run again and you will be prompted for each script in turn. The conversion process uninstalls all your currently installed mods and then attempts to reinstall your mods one at a time. When upgrading to version 0.50.0 NMM needs to convert all your currently installed files to the new method.
With the introduction of version 0.50.0 of NMM we've changed the installation method for mods installed via NMM as well as their unpacked location.
