What is my phone actually doing when it says optimising apps after an update Technology

It is translating your apps into a form your specific phone can run fast, and it has to redo it because the update changed the thing it translates against.

Apps are shipped in a portable intermediate form so that one download works on many different phones. Running that form directly is slower, so at install time the phone compiles it into native machine code for its own processor and stores the result. That compiled copy is what actually runs when you tap the icon.

When the system updates, the runtime libraries underneath change, so every one of those stored copies is stale and potentially invalid. Rather than have every app be slow the first time you open it, the phone does the whole batch up front. That is the counter you are watching.

Nothing is being scanned for problems, nothing is being deleted, nothing is going anywhere off the device. It is a build job. The reason you should not interrupt it is simply that it is doing heavy work and yanking power mid write is a bad idea, not because something delicate is being repaired.

The battery drain afterwards is the same story continuing. Caches and search indexes get rebuilt in the background over the following day, and then it settles.

Modern versions are lazier than they used to be, which is why the step is much faster than it was five years ago. Instead of fully compiling everything on day one, phones increasingly compile the parts you actually use, based on watching how you use each app. So the count going up quickly is not it skipping work, it is it deferring the work you may never need.

Same family of idea as a desktop rebuilding a search index after a big update, or a game shader compilation screen before you play. All of them are one time work done up front so the thing you actually do afterwards is fast.

If it takes twenty minutes with a few hundred apps, that is normal. If it happens on every reboot rather than after updates, that is not, and it usually means storage trouble.