Later researched and found that the issue is with custom kernel provided by GCP / AWS. The issue has been solved by following procedure:
1. Remove GCP / AWS kernels
For GCP:
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sudo apt-get remove linux-image-*-gcp
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sudo apt-get remove linux-image-*-aws
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sudo apt-get -y install linux-image-generic
sudo apt-get -y install linux-headers-generic
4. Run disk checking schedule and voila. Quota is back.
I though this maybe usefull for someone facing same issues with VMs hosted in GCP / AWS.
Also, please let me know whether I did everything right?
Thank You.