The trial court can alter the charges against the accused, but it has to be clearly explained to him by the trial court as has been provided under section 216 Cr PC. But If the trial court has failed to explain the altered charges, then the accused can submit the application at or before the stage of section 313 Cr PC.
Any suggestion depends upon the facts and circumstances that necessitated the alteration in the charges. The alteration or addition is always subject to limitation that “no course should be taken by reason of which the accused may be prejudiced either because he is not fully aware of the charge made or is not given full opportunity of meeting it and putting forward any defence open to him on the charge finally preferred.”
But, that's not the query. The querist has asked, "can accused file (fail) application under section 216 Cr PC at the stage of 313 Cr PC"? And if the querist meant that the accused failed application under section 216 Cr PC, then the answer is that the trial court was satisfied that accused has understood the altered charges, hence no need to explain him, and no prejudice caused to him.