Help! Engine misfiring!!!
 

Took my car to the shop yesterday with a worn clutch.

They called me today saying they had trouble starting it (took ~30 seconds), and when it did it threw a misfire code (blinking CEL) and now they want to do a coil replacement!

MY OPINION: the engine had trouble starting because it was flooded; it is the middle of winter right now and I saw the tow truck guy turn it off before it was warmed up yesterday

I am a bit wary of getting a coil replacement as it is another $400!
Basically I am wondering will the engine misfire code go away or is this actually a serious side effect whereby I need the new coil now?

How many miles on your current coils? If they are going to charge you $400 for them you should just buy the BHR upgraded ones and install them yourself. They are a bit over 400(485) but they are much better than the oem ones.

do it yourself either way

you can do a more serious de-flood. In the aviation world spark plugs are around 75 dollars each and we have to do a oil lab test including the oil filter every time the oil is changed. (the 25 dollar one that gets done on the 8 is a joke comparitively). On that note you can do the proper entire deflood process.

Before you do this, crawl under your car, and double check you have the right starter. Actually check the part number and make sure its been upgraded. After you do that, check to make sure your engines at the right flash and that the battery is still ok. By ok I mean actually get the battery bench tested. If all three of those turn out to be normal then do a proper flood. Removing and cleaning spark plugs, and while your at it, you can seafoam the engine too and kill two birds with one stone since your already going to all the trouble.

it doesn't matter if the car is turned off cold. I've TRIED to flood my car, literally turned it on, backed it into the driveway, turned it off and still can't flood it.
If yours is a late 05 or newer it most likely has the upgraded starter, battery, and plugs.

with that said, if you're going to pay $400 for an ignition system it had better be a BHR kit or you're crazy.
coils are about $30 each and super easy to swap out yourself. (we have a step by step if you do a search on here)

to answer your question: misfires don't just go away but all engines occasionally misfire so maybe it was a fluke? doubt it but possible.
how old is the car? last time plugs, wires, or coils were changed? you sure all the spark plugs are properly secured to the plugs? (ours have been known to come loose if not properly installed)

My advice: if you have over 25,000 miles on your coils or plugs, it is worth looking into replacing them.