Oil is a big deal with Sprinters. Many of us, myself included, change our own oil. For a few different reasons.
A few thoughts ...
1. I would never get my oil changed at jiffy lube. I doubt they used the right oil. They probably used some type of diesel oil but not the low ash spec stuff that's required. Consult your owners manual. I use Mobil Mercedes spec ..
2. After each oil change its a good habit to check your engine oil level. I do it each & every time. Even though I've placed the proper quantity in, it's a good way to check for leaks. What if the drain plug or oil filter weren't secured properly, etc. Anyway it's a good habit.
3. On my 3.0 engine the correct quantity is 13 qts not 12. Again, check your owners manual. Pay attention if it states liters or qts. If you've only been placing 12 qts in, there's your problem right there. Running these engines with low oil creates all sorts of problems.
4. If you had a very low oil level, I would think you would get an engine warning light. I don't believe the tune will interfere with that. If it did .. bad choice in which tune was purchased.
5. The guy that did the tune gave you bad advice. There are good shops and bad shops, dealer or not. It's best to do research & find the good shops. Sprinter-source is a very good resource. If in unfamiliar territory, I can always call a shop and ask a few very specific questions to get a feel of its a good shop. First question is, how long have your techs been working on sprinters!? I want the resume of the guy that I'll be hiring to work on my van.
What makes you think the engine is fried? Did it seize? If you need a new engine start hunting for a low mileage used one. Start looking all over the country .... needle in a haystack.
Two phases to a tune ... hardware & software. I believe the tune software is engine specific, so if you drop in a new engine I believe you'll need to purchase the software again. Check with the tune shop.