Hi, This is actually not a limitation. It is by design.
One of our principles is not to modify users' policies automatically. We leave that to the user to decide on his policy architecture.
So once you got rid of all of your Pre-R80 gateways that have IPS blade enabled, your policy will still remain as before. We definitely recommend on unifying your threat prevention rules into one policy, manually:
1. On the Threat Prevention layer, make sure that your gateway will be matched to the appropriate profile (either since the "install on" is "any" or if it's your specific gateway, as well as one explicit rule with "any" in the protected scope). If this is not the case, create such rule.
2. Go to your IPS layer and delete the gateway rule.
3. Once you have removed all of your IPS layer rules, the IPS layer will disappear.
The reason why this process does not happen automatically, is because users might still be interested with a layer per threat prevention engine. Some users may also want to use the "protected scope" column to create specific threat prevention profiles to different scopes. So the decision stays in the hand of the user.
Please let us know what are your thoughts on this behavior.