Had the same problems, so after I recreated a ssh file and rebooted, I ran the raspi-config program via ssh, and selected #3 Interface Options, and then selected SSH option and enabled SSH. It has been working since, even if the ssh file is missing from /boot. Hope this helps and you have fun improving your system.
Last I knew, the SSH file you placed in the config disappears from the config since it has server it’s purpose and you should be good to go from there on out. NTW
This sounds like you have a more general network problem rather than it being the ssh file.
I suspect that just restarting the pi will restore things without you adding the file again.
When it fails, can you ping the pi?
Are you on a wifi or ethernet connection?
Are you on a static or DHCP ip address?
It might be a DHCP address not being renewed when its lease expires.
Is your DHCP lease time 24hrs?