An announcement was made earlier that changes would occur in september with certificates that would be deprecated and we are down on all three servers is there anything we can do this is
a crisis for us
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Have you tried rebooting? All of your servers appear to be responding to basic TLS requests with the now expired R3 chain. I'm not sure why the full web requests would be timing out though. Do they connect to any back end servers over TLS as well that might be failing?
2008 R2 is way out of support at this point. So there hasn't been a lot of testing on how this expiry would affect it. But the reboot may force IIS to switch to the newer non-expired R3 chain.
If not, you may need to do some checking in the Windows cert stores to make sure the ISRG Root X1 cert is in the Trusted Roots store and possibly some additional tweaking in the Intermediate store.
our servers are 2008 R2 and we need certs at this point - if we can't get the lets encrypt cert to work with reboot - do you have any additional suggestions?
The cert itself isn't the problem and I'm sure we can make it work. It should just be a matter of getting Windows to build and serve the correct chain.
There are two main things you need to verify if it's not fixed after a reboot.
Is the system time on the server correct (including timezone)?
Open certlm.msc, expand Trusted Root Certification Authorities - Certificates and make sure there is an entry for ISRG Root X1 that is also issued by ISRG Root X1
If both of those are true and it's still not working, we can dig deeper.
If the reboot doesn't fix it, check this post out. Clearing the extra R3 cert from the system user resolved an issue for us just now where IIS was sending an incorrect intermediate.