The duplicates can't be removed. it will delete the original module as well if the duplicate is removed.
and i've tried to update this Simplex to 2.5 on 3 different installations and all having the same issue.
When i tried with other Shape5 templates, none was facing this issue
is this a coincidence?
This isn't a bug with the template, it sometimes occurs in Joomla when migrating from 1.5 to 1.6+. The only way to get past it is to remove the duplicates.