First of all, I would like to know how much % of FBS you are using for your culture? 10 or 20%?
Secondly, try to use GlutMAX instead of L-glutamine.
Now, coming to the transfection experiment, you will be using OptMEM or serum-free media (or minimum % of serum), right? So, cells will be already under stress, so please do not add any extra stress by not adding glutamine, you can add Glutmax. The cells will be fine.
I personally feel you should not skip the glutamine in your culture.
Thank you for your feedback. To answer your question in regards to FBS, I plan to use inactivated FBS with 10% concentration. I take your advice and proceed with glutamine in the media. I am using the optimized calcium phosphate transfection from this paper: Article Optimizing Conditions for Calcium Phosphate Mediated Transie...
I'm sure that many people have made that mistake soon corrected after addition of glutamine. Alpha-cetoglutarate and glutamine levels very important to DNA demethylation (TET enzymes).