My understanding of what you are doing is building an array of the control references in the main vi to pass to the sub-vis. Is this correct? If so, why not bundle the references instead? This way you could easily pull out the required reference by name.
Aside from that, if you are passing references to the front panel objects you shouldn't need to close them at all. The following links should be useful in helping you to understand when to close references:
http://exchange.ni.com/servlet/ProcessRequest?RHIVEID=101&RPAGEID=135&HOID=506500000008000000834C0000&UCATEGORY_0=_49_%24_6_&UCATEGORY_S=0&USEARCHCONTEXT_QUESTION_0=closing+references&USEARCHCONTEXT_QUESTION_S=0
http://www.ni.com/devzone/lvzone/dr_vi_archived4.htm
Hope that helps.
John