That is a tough one. My guess is something to do with NAT somewhere because of the variations.
Does the Data Centre MX have a private IP address, and is it sitting behind something else doing NAT?
If so, the device doing NAT might be expiring the NAT entries after a certain amount of time (or perhaps on last usage).
If this case applies, you could test this out by changing the DC to using manual NAT traversal and setting up a specific port forward for AutoVPN on the device doing NAT.
https://documentation.meraki.com/MX/Site-to-site_VPN/Site-to-Site_VPN_Settings#NAT_Traversal
Are the spokes sitting behind a CPE doing NAT? If so, is the CPE in use the same for all the affected sites?
If so, check out firmware versions on the CPE. Maybe even try a different model CPE.