@Saurabh I am only running into this issue when I load the entire list of stores "12,000". Everything works just fine when the total store count is around 8,000. Once I cross the 8,000 limit, I start getting this error. I have only imported the stores + logo so far and started experiencing this problem. I have not uploaded the items + images that totals in hundards of thousands.
I am also noticing that the delivery guy is also showing offline on/off.
I believe performance related issues maybe the root cause. If you would like to take a look, I will gladly give you root before I move everything over to AWS. Below are the virtual private server specifications from namecheap.com
CentOS
4 CPU Cores
6 GB RAM
120 GB SSD RAID 10