Where is the user crontab stored?

Actually, it's not recommended to handle those files by hand. Per crontab man page:

Each user can have their own crontab, and though
these are files in /var/spool/cron/crontabs, they are not
intended to be edited directly.

Files under /var/spool are considered temporary/working, that's why they probably get deleted during an upgrade, though a closer look at the cron package's upgrade scripts may shed some light on this.

Anyway, it's always a good practice to back up your cron entries or keep them in a file in your home directory.

I assume you're using crontab -e to create crontab files on the fly. If so, you can get a "copy" of your crontab file by doing crontab -l. Pipe that to a file to get a "backup":

crontab -l > my-crontab

Then you can edit that my-crontab file to add or modify entries, and then "install" it by giving it to crontab:

crontab my-crontab

This does the same syntax checking as crontab -e.

Its stored inside /var/spool/cron/crontabs folder under username.

I finally found out why my crontabs and Postfix installation kept breaking after boot. It's a really stupid reason but...

I had /var/spool mounted as a tmpfs RAM-drive.

Sounds idiotic and it is, but I had followed one of the old SSD-tweaks to lengthen the life of my SSD. In doing so, I blindly mounted /tmp, /var/tmp and /var/spool as tmpfs without thinking of the repercussions. I thought /var/spool was like /proc/ or /run/ and that it was only useful for the duration of the session. I was clearly wrong.