Income tax refund issue in case of wrong form 16

Recently, I received arrears from my ex-employer and filed Form 10E with the IT Dept. based upon details shared with me.  However, the Accounts Officer has not mentioned tax relief u/s 89 in the Form 16 released to me. I have been making due follow-up with him as well as with his seniors to issue revised Form 16, but not getting any satisfactory response.

So, the zero tax relief u/s 89 mentioned in Form 16, is not going to match actual tax relief to be mentioned in Income Tax Return (ITR), through Form 10E.

Whether I would get tax refund without any problem, given mismatch in Form 16 and ITR?