You need to override both files, the included file and the file which includes.
In the line where {include}
is used the path must be:
{include file='../_current_dir_/_file_.tpl'}
e.g. you want to override cart rules template:
override/controllers/admin/templates/cart_rules/informations.tpl
Then you need the template which includes it. form.tpl
(in this case):
override/controllers/admin/templates/cart_rules/form.tpl
Inside form.tpl
you need to change {include}
of informations.tpl
to:
{include file='../cart_rules/informations.tpl'}
Even both templates are in the same level it is for some reason needed to go one level up.