Change sample names while using cummeRbund
Don't know which file was used by cummeRbund for sample names but replacing q1,q2,q3 and q4  with Batis, Blue_silver, Chakwal_50 and Syn_22 for all the files in the directory containing cuffdiff output worked for me. 

I used sed language for this as shown below:

sed -i 's/q4/Syn_22/g' *


Or more generally you can use 

sed -i 's/sample_name_shown/sample_name_to_change/g' *


After that I deleted the sqlite object created by cummeRbund and again created this object using readCufflinks() in R.
This time sample names are changed as desired:

samples(cuff)
sample_index sample_name sample_name parameter value
1            1       Batis        &lt;NA&gt;      &lt;NA&gt;  &lt;NA&gt;
2            2 Blue_silver        &lt;NA&gt;      &lt;NA&gt;  &lt;NA&gt;
3            3  Chakwal_50        &lt;NA&gt;      &lt;NA&gt;  &lt;NA&gt;
4            4      Syn_22        &lt;NA&gt;      &lt;NA&gt;  &lt;NA&gt;