deleting the .zim folder is no problem. I sync between different machines using
git and have the .zim folder in my .gitignore file. Obviously I end up with
outdated .zim folders this way. However I can simply delete the whole .zim
folder and do "Tools -> Re-build Index" and everything gets recreated.
See http://zim-wiki.org/manual/Plugins/Version_Control.html for details about
this way to sync.
I would welcome some better solution (regarding the .zim folder) -- perhaps
Jaap can suggest something.
I cannot reproduce your problem with links on Linux however. It works as
intended. You should probably file a new bug on launchpad at
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