I think I have found the answer already: it looks like you need to "save" (or rather: re-save) the project after manually confirming individual segments and before realigning. This prevents the confirmed segments getting lost. It makes sense, but it's not in the instructions or video.   I am a compulsive saver but saving my alignment project of 2000 segments takes fairly long (i.e. coffee or bathroom breaks). I had wondered about this, tried it, and sure it worked.

I have to correct myself: the saving doesn't take long, at least not anymore; it just starts slowly.

Unknown said:

it looks like you need to "save" (or rather: re-save) the project after manually confirming individual segments and before realigning. This prevents the confirmed segments getting lost. It makes sense,

Actually not, from the UX perspective it does not make sense at all. This looks like a result of the typical "programmer's perspective" (from which it does make some sense, indeed).

Unknown said:

it looks like you need to "save" (or rather: re-save) the project after manually confirming individual segments and before realigning. This prevents the confirmed segments getting lost. It makes sense,

Actually not, from the UX perspective it does not make sense at all. This looks like a result of the typical "programmer's perspective" (from which it does make some sense, indeed).