A Tower Controller reported an aircraft landed with landing gear malfunction indications.

Narrative

I was working LOCAL and Controller in Charge (CIC) combined. Training was being conducted on Ground Control. A DA42 wanted to do a low approach; because he was worried about his gear. He did not declare an emergency. He did a low approach over the runway; the ground control and myself checked his gear. I told him; 'All gear appears down.' He landed and said he was not sure if the wheel was coming off. I asked him if he could make Taxiway 1. He said he could; but almost got there and then said he could not and he got off at the inactive runway. He pulled on to the inactive and I asked if he could go farther up the runway. He did and then said he had to stop because he was scared that the wheel would come off. I told him would would get him assistance. There are no hold lines on the runways to show where the Runway Safety Area (RSA) is and I had to use my best judgement that he was out of the safety area. I had an aircraft that needed to depart and one that was in bound. I told both aircraft to use caution for a possible aircraft in the safety area of the runway but not on the runway. We also have a LOA that says we can operate on runways with personnel and equipment in the RSA. They took off and landed with no incident. I then called management and double checked that we could still continue with operations. They said I was good and to give a cautionary to all aircraft. I continued to work traffic departing and landing aircraft. When management called and said they were closing the airport; I stopped operations. I would stop operations until the aircraft was off both runways. I would then call management before launching any aircraft.