tax calculation common rule

I got a mail from HR department of my office on 11/04/2014 to update the payroll site to declare the flexi option ( Medical, Lunch Allowance, LTA, NPS ) before 21-April-2014. But, unfortunately due to busy travelling schedule I have missed to update it. After that, I drew their attention after few days ( first week of May ), but they denied to allow me to update.

Even after publishing new union budget on July14, they only allowed me to update the Investment Declaration.

As a result I could not avail the tax benefit for the whole year.

Now my question is 

1 )  Is there any government rule, by which salary structure can't be restructured ? If, so then what is the specific period ? Did they follow govt rule or own HR rule ?

2 ) Can I claim the benefit of  LTA ( Block period 14-15 ), Lunch Allowance, NPS at the time of filing return ?

These are such kind of things, happens with many employees and has to accept HR rule silently. Can anybody answer these ?




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