Yeah Mendix doesnt use the Windows certificate store at all for outbound calls. It uses the Java truststore (cacerts). So importing certs into the Windows store wont help for the REST call Mendix is making.
You need to import the full chain (root CA and any intermediates) into the cacerts file of the JRE that Mendix is using. Something like:
1. Find which JRE your Mendix runtime is using (check the service config or runtime settings).
2. Run keytool -import -alias somealias -keystore "path/to/jre/lib/security/cacerts" -file yourcert.cer with the default password "changeit".
3. Do this for both the root and intermediate certs if they are missing.
4. Restart the Mendix runtime.
This is almost certainly the issue since you said you only imported into the Windows cert store. Also worth noting that Mendix 9 ships with a newer JRE (AdoptOpenJDK 11) compared to older versions, and the default cacerts bundle might be slightly different from what you had before. So certs that happened to be trusted in the old JRE might not be present in the new one.
You can verify whats in the truststore with keytool -list -keystore cacerts and grep for the CA you need.
https://docs.mendix.com/developerportal/deploy/certificates/