Ok, let's reason this out! To be fair, I'm dumber than a rock so take what I say with a huge grain of salt...
1. What's the reason for marking the flywheel when you take it out?
I suspect that when the engine's at the manufacture plant they can balance everything as close as possible with the OEM flywhee. Marking the relationship of the flywheel to the crank preserves this relationship.
2. Is this a big deal?
Humm..... I don't think so because IMHO what happens when you resurface a flywheel? Why you've just destoryed the OEM balance. Of course as the flywheel was warped and worn the OEM balance was destoryed over time anyway.
3. What do I do now?
Well... when you buy a new flywheel you don't run down to the loacal auto machinest and have the flywheel trued or balnced in concert with your engine, now do you? You just bolt thing on and go! What's the differnece here?
4. Well the flywheel won't be balanced!
Hummm... were that the case changing one would be a death sentence. The engine would vibrate itself apart and self destruct. Then of course when you look at the flexplate... you may see drill holes where metal has been removed or weights welded on the plate... Yep, it's balanced!
Bolt 'er back on, use some locktite on the bolt threads and quit worrying...a nd save that for other more important stuff.