I need to clean my Lego including minifigures, printed pieces and cloth pieces from smoke (apartment fire). I have found that soaking the pieces in isopropyl alcohol removes the smell, but am I damaging the pieces by soaking them for 1 or 2 days?
First of all, sorry for your loss and we all wish you good luck recovering your bricks!
As for cleaning LEGO bricks, if you need to remove physically visible dirt, here you can find lots of tips on doing just this, or you can go over to the official LEGO website and heed their recommendations.
If the only problem is the smell of smoke, there is another question about getting rid of foreign scents, maybe you could find valuable information there. If I were in your shoes, I'd try the less aggressive, less risky methods first, and only gradually progressing towards the inorganic solvents if all the previous steps have failed.
There is a similar question over at Chemistry.SE, they might be more knowledgeable than us. But even if the ABS material of the LEGO bricks prove to be immune to the deleterious effects of alcohol, the minute amounts of other ingredients, coloring pigments or printed details might fare worse. LEGO however, recommends cleaning electric parts and pieces using alcohol though, but they specifically mention wiping, not soaking, and especially not for prolonged periods.
But if you really intend to use the alcohol bath, I'd recommend that you pick a few "volunteers" who will test the method before you apply it to the general populace, therefore only risking your less precious, more easily replaceable pieces.
Washing LEGO ABS and Polycarbonate (PC is used for clear and colored transparent parts) bricks and parts can be done safely in a normal mixture of dishwashing liquid and clean water, preferably distilled water, of luke warm temperature. Leave the bricks and/or parts in for a short while and a toothbrush can be used for brushing off all dirt. Allow the parts to dry thoroughly, that's my method and it works fine. Most of the possible odors will be gone as well. This method prevents damage that can occur in due course if the parts are washed in a dishwasher as the formula in dishwasher tablets or the like differs a lot from normal dishwashing liquids, dishwasher tablets contain far more aggressive ingredients than dishwasher liquids all have. As a side effect, dishwashing liquids leave a thin layer of anti static material, making the bricks easier to take apart and their appearence is fresh and shiny, almost like new. And using distilled water leaves no staines on the bricks.