"Hot trub is that part of the break that occurs during the boil and is mostly proteinaceous; cold trub, which consists of proteins and protein-tannin complexes, is formed as the wort cools and the beer settles (1). Although most amino acids are assimilated by the yeast, remaining proteins should be removed because they later react with polyphenols, resulting in colloidal instability (haze). The elimination of all non-amino acid proteins is not warranted or even desirable, however, because they are essential for giving the beer full body and head retention."
A little quote from Ron Barchet. And NO, the hot break and cold break protein will not absorb back into the beer if you leave them in the fermenter. As you can read, the amino acids are used up by the yeast. The Proteins which do not settle out, do not settle out because they are very small and float easily. These small proteins would not strain out even if you tried. These very small proteins are the cause of Haze. We all know that that is not a death sentance for beer.
Now there is a huge difference in all-grain and extract brewing when Hot Break and Cold Break is concerned. Extracts already have a large percentage of the proteins removed during manufacturing. All Grain brewer must take time to skim the brew pot and try to remove as much hot trub as possible. It has been shown that quicker, less-intensive mashing routines yield worts containing more trub. Conversely, triple and double decoction mashing produce worts with considerably less trub, because the mash boiling process and the extended protein rests of such mashes maximize the breakdown of proteins and the removal of trub before the kettle boil. But... There will always be some that makes it into the fermenter because the proteins are usually 10-50 microns in size and a strainer or grain bed will not get them all.
What do we do to get rid of the left over hot break material that is in our wort? Well that is what a cold break is for. All the cold break is is the step for removing the smaller floating proteins. Cooling the wort quickly causes them to fall to the bottom of the pot, where you can siphon or pump from above the trub leaving most of it behind.
But then again there are always going to be leftover proteins that make it into the fermenter.
What do we do to make these leftover hot break and cold break proteins precipitate to the bottom of the fermenter?
That is where we use Hop Backs or whirlpools to get the rest. Or is it worth the trouble? I don't think it is worth the trouble. I prefer to use Irish moss or chillproof to help the proteins precipitate out.
If you are really anal you could use a 1 micron filter when you transfer from the brewpot to the primary....that will remove the protein. The thing is that most people filter after fermentation. Why? I feel that they want to leave the amino acids to help the yeast. I have done it both ways and I cannot tell the difference. I brewed 2 identical batches and purposely left all the break material in one and omitted any haze removers. One ended up hazed and one was clear. In a blindfolded taste test, I concluded that there was no difference in taste. I was looking for bitterness caused by the proteins. Some experts say that they can cause bitterness and poor head retention and other say absence of them will cause poor head retention. I did not see it either way.
I weigh the amount of effort required with the results. I see no need to go through a bunch of trouble to try to remove all the hot and cold break.
Now as a side note. I left the hazed beer in the keg and refridgerated for 2 months and then tapped it. The beer had cleared. And a second unblind taste test between the 2 beers was unable to tell the difference. I concluded that the hot and cold break proteins only affect the beer by adding haze. Which can be overcome with additives and time. No affect on the taste was seen. Now I will admit that this test was limited, there may be styles of beer whos taste is affected. The verdict is still out. But for my house brew....A Brown Ale, there is not difference.