I used to work for one of the largest home-electronics manufacturers, and I dealt quite a bit with the batteries and charging, and I can explain how we reasoned when it came to protection circuitry.
1. Once a cell has been discharged beyond a certain point (varies between cells, even within the same chemistry), it's _bad_. The tolerances have been exceeded, and you're working outside of what the cell-manufacturer has tested and what the datasheet says. Ergo, as a manufacturer that takes responsibility, and actually care about our customer (and fears lawsuits), we have to make sure that the cell is not used again, as I could cause (in worst case) fires.
Dell, Fujitsu, etc know this all too well...
2. Replacing the cells in a pack is _way_ beyond what their intended use is, and to be honest, I wouldn't even do it myself.. Why? Am I chicken/boring/inept? No, because, the likelyhood of me finding the _exact_ same cell to replace the failed ones is close to impossible. No, having the same formfactor and chemistry is not enough. The charge algorithm is tuned _exactly_ for the cell that it shipped with. And the cells that we shipped with were pretty darn good, so sourcing the same from a random internet-site is near impossible. Meaning, if you put a lesser specced cell in there, it will overcharge, over discharge, overheat, depending on how much the cells specs are off.
We easily spent a month _per product_, just fine-tuning the parameters. And that's not counting the hundreds of cells that spend a few months verifying the end-result.
And, frankly, if you do change the cells in a pack, and get it working, and it burns down your house, your insurance will find out. We did forensics for things like that, as the insurance-companies liked to go after us (usually chargers though, but the occasional batteries as well). As we don't like getting blamed for things we didn't do (both us engineers, as well as our lawyers), it was important for us to figure out. Most of the time it comes down to "this wasn't ours", but we saw "poor repair jobs" as well, for parts that we simply didn't perform repairs on (packs and chargers are both such items, as it's more economical to trash them and send new ones).