Flooded a I6 4.0? Permanent Damage?

So this wasnt my jeep that this happened to. Its my buddies 98 4.0 ZJ, but there was a big mud hole on a trail and we measured it with a stick in the mud in the center and walking into it, it only went up about 3/4 of the tires (31" M/Ts dont know brand) so he decided to go for it, we didn't know at the time but the tracks in the hole were super deep and he went into them about halfway through the hole and the mud went about halfway up the headlights, the jeep shut off after gurgling for a few seconds in the mud, he kept it off until we got it out of the mud, (I pulled him out with my ZJ). He let it sit for a few minutes while he changed (he was caked in mud) he turned the key and it struggled to start for probably 3 seconds (kept turning over) and then it started up shooting a lot of smoke out of the exhaust, he gave it some gas and held it at about 2500 RPMs to get the water out, it idled for probably 10 minutes before he got in and drove it to the trailhead. When we got there it was still dripping water from a (new) exhaust leak. We left the trail and headed to the coinwash. It seemed to start fine from there so I'm like 90% sure it's ok but he asked me to check on here.

TL;DR Buddy sank his 4.0 ZJ halfway up the headlights, idled for a 15+ minutes after getting out of the water. Any permanent damage that can be told from this?

Flooded a I6 4.0? Permanent Damage?