Far be it for you being the first to do this. I've had 20-year+ mechanics unintentionally remove head bolts. It's not the worst thing you can do.
You have done the right thing to retighten the head bolts. Although I've seen people try reusing head bolts, that is a fool's bet. If the block or head have been heat-warped, the head gasket probably popped loose when the bolts were removed. And if you are one of those that say, "It never overheated.", you have to keep in mind the temperature gauge on the dash is a liar.
So, you might buy a new set of head bolts (about $45), and the engine starts leaking water or pressurizes the coolant system. So, there is no guarantee. You might get lucky; might not. But you won't make that mistake again...
If the old head bolts have been retightened, get the new bolts, remove the old bolts, one-at-a-time, and install new head bolts. Oil the head bolt washers and the threads of the bolt with 30 wt oil, or whatever is handy. Start at the center of the head, working in an X pattern, tighten each bolt to the second pre-load number; 44 ft lbs (60nm), removing each old bolt, and tightening in the new one. Then, proceed with the two 90 degree turns, again, working in an X pattern, tightening from the center to the outside.
There are a lot of turns and it's easy to 'get lost', especially on the final two TTY turns. Once the pre-load is set on the head bolts, I mark the top of each bolt with a yellow paint stick, at the 12 o'clock position (manifold side of the head bolt). Then you can easily see the 1/4 turns to 3 o'clock and finally, to the 6 o'clock position. It's best to use a long breaker bar for the final turn. It is up around110-115 ft lbs.
If the any cylinder loses exhaust into the water jacket, you will have a overflow tank that will pressurize. You may see oil in the overflow. Your coolant level may go down. If any of these issues happen, the replacement head bolts did not work and your head gasket broke loose and will have to be replaced. In spite of some reusing a head gasket, that's absurd... I would say you also probably should affirm that both the cylinder head and the block are truly flat. One mention of the head gasket embossing the head, that would be normal, as it is aluminum, but that embossing also happens to the block, and that can cause the assumption the block is flat when it is not.
The other 'common cure' is to use either higher torque head bolts or ARP studs, which personally, I have fallen out of favor with. The problem with doing a 'bandaid patch', is although the ARP, RaceWare, or the Opti-Torque I am currently using; although you can get bolts that cost more than 4 times as much to clamp the head down, the extra torque will also distort the block so the rings no longer fit correctly in the top 1" or so. Attempting to make a cylinder head flat by pure brute force can do more damage than good. Also, there is the incident of cracking the block's bolt holes, which is the death of the block.
I would try the simplest, cheapest fix. New stock head bolts. If that fails, you have to remove the cylinder head, rework the head and make sure the block is flat.
If I can be any additional help, cylinder head work and the particulars of these TDI's are my skill set.
Good luck.
