In Org mode, how do you log progress in multi-day TODO items?

I use `org-clock-in` to the task I'm working on, then a simple `clocktable` with some dates will show me exactly what I worked on. `Clocktable` has depths so you can get as much granularity as your notes take you. Maybe I'm missing the point of the question, but I do this with multiple files without any problems and I can get a table of the work I did for the entire year, a single sprint, or IP. Sorry if I'm telling you something you already know.

Take a look at `org-log-done` and `org-log-into-drawer`. These will tell org to log the date and time when an item's status is changed (you can specify). When the agenda is built you can show all these logged items on the date they were completed with `org-agenda-log-mode`, `org-agenda-log-mode-items`, and `org-agenda-start-with-log-mode`. This allows me to place TODO items anywhere I want (my logbook, notes, and a scratch list) and as I complete them through the week they're all shown in the agenda according to when I completed each. Perhaps this is unrelated, but it is also useful to remember that when capturing to a datetree structure there's no reason you can't have different dates in the datetree and the time-stamp. I use this all the time. The date in the tree is the date the item was captured, and the time-stamp is when I want it showing up in the agenda. Maybe that's of limited value to most people, but the point is that the datetree and the time-stamp (thus: date on the agenda) are two separate concepts.

I add: #+STARTUP: lognotereschedule logdrawer #+SEQ_TODO: TODO(t/!) IN_PROGRESS(i/!) HOLD(h@/!) READY_FOR_QA(r@/!) | DONE(d@) CANCELED(c@) To the top of my org files, then I can set a TODO to the IN_PROGRESS state for things I am currently working on. I use `org-clock-in` and `org-clock-out` to track time in a `:LOGBOOK:` drawer on that particular "task". Then I have a heading like this: ***** 1/3 - 1/7 #+BEGIN: clocktable :scope file :block 2022-w1 :step day :maxlevel 5 :compact t :emphasize t :stepskip0 t ... #+END: which creates a day-by-day summary of the time I worked on what tasks. On Friday, I can look at this and see what I did over the week. HTH