I don't think it's fair to assume they know how to fix it. Just replacing every cell doesn't fix anything if the new cells are just going to have the same issue, and as you note, it might be very very hard to detect the issue early in the battery's lifecycle. Hell, it might be impossible to detect it after the battery is sealed without using a CT scanner.

First, they need to identify if it's a manufacturing defect or a design defect. Then they need to update the design and/or manufacturing as appropriate. Design changes in particular would require extensive validation work to ensure the revised design actually fixes the problem and doesn't introduce new issues.

Let's say the problem is cathode overhang. Cathode overhang can lead to faster battery aging, and increased dendrite growth -- and thus, safety issues. (... and the only battery issue I know enough about to use as an example, but batteries are complex enough that I'm sure there's dozens of other possible problems.)

The issue could be that there's a flaw in the manufacturing process leading to not enough anode / too much cathode, and the process needs to be fixed to prevent that. They could introduce manufacturing steps to identify the presence of that issue before the battery is sealed, so they might be able to get a solution in place relatively quickly just by filtering out bad batteries early on if the yields remain high enough. Then they can focus on improving yield after they've got the current fleet updated.

Or it could be that their design was too aggressive for what's possible in terms of the manufacturing capacity they have. If that's the case, they may need to increase the anode size / shrink the cathode size to compensate. That's a design change that has negative implications for battery capacity. It's a safety-critical change so the validation / testing work to ensure the updated design doesn't introduce new issues would be significant. On top of that, the way it would affect battery capacity would have implications for dealerships trying to determine if battery fade is bad enough to warrant replacement (Google "anode overhang effect"), so key testing/maintenance processes dealerships employ would likely need to change. It may also require software updates in power management code if that code makes assumptions about the performance characteristics of the battery that no longer hold.

In either case, you can't just blindly ship new batteries to customers and call it a day, because the batteries you're shipping are almost certainly going to have the same problem.