The default behavior is for missing I/O to cause a FATAL error (typically desired, as you stated). However, if you want to switch it back to RUN, you have to use Designer w/Mode switch in Term position, or possibly powercycle the PLC with the Mode switch being in RUN position, but this has its own set of concerns (e.g. cannot change mode via Designer software until you move the switch back to TERM).
Another possibility is to change the missing I/O condition to be NON-FATAL error. This can be done as part of your System Configuration. HOWEVER, YOU ARE RESPONSIBLE FOR WRITING LOGIC THAT DETECTS THIS ERROR CONDITION AND HAVE YOUR PROGRAM BEHAVE ACCORDINGLY.
The PLC will stay in RUN mode and continue to run WITH FAILED I/O. I do not know if this is acceptable for your application. Even if it is, you have to realize that there can be different causes for failed I/O, but the PLC cannot distinguish between a bad comm cable, failed Ethernet switch, or bad hardware, or ...
Regardless, failed I/O is a critical situation and must be handled properly and safely.
Remember that minimizing or eliminating the failed I/O event would be the safest/best solution.