Welcome to the community :)
To my knowledge if you mark the item lost on the 'edit item' screen, it
won't be returned from the patron's account. If you do it from the
'items tab' it will be checked in. So you should only make it visible if
you are aware of the different behaviour and that is intended :)
http://bywatersolutions.com/2015/02/23/lost-koha/
Hope this helps,
Katrin
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