… When I am finishing the layout of a score and adjust the percentage of each staff …

Generally, it is a bad idea to resize the staves individually.

Instead, avoid resizing the staves, and resize systems (or pages) - so that all staves in the same system (or page) get the same size.

The only exception is a score for e. g. piano and solo instrument where you keep the piano Grand Staff at “normal size”, but set the solo staff at a smaller size.

… the resizing only affects until some arbitrary measure even if I carefully choose to resize the staff until the end of the piece. After that point if I want the music to remain the same size I have to try to guess a new percentage that might produce the same size music …

Without examining the actual Finale document I can only guess.

My first guess would be that you are not aware of the document’s default page format settings (for new systems/pages):

Document menu > Page Format > Score…

You should examine the settings in Page Format for Score, and make sure the settings are as needed. *)

I repeat:

The settings in Page Format for Score are the default settings for new systems/pages.

Already existing systems/pages are not affected (= you can freely re-format already existing systems/pages).

When you have adjusted the settings in Page Format for Score (so that all new systems/pages will be correctly formatted), you may need to update some of the already existing pages with the new, adjusted settings.

To do so:

Page Layout Tool.

Select a region of pages, and go to

Page Layout menu > Redefine Pages > Selected Pages of Selected Parts/Score…

*) an option that may be helpful:

Page Layout menu > Update Page Format for Score

When the option {Update Page Format for Score} is toggled on, Finale will monitor your layout edits (e. g. when you change page size, or scaling, or system margins), and update the document’s default settings in Page Format for Score.

NB:

The option {Update Page Format for Score} is program specific, not document specific.

When you have used {Update Page Format for Score}, you should probably toggle it off - before you begin working on other Finale documents (to avoid un-expected surprises).

Thank you for your answer. My file is what you called the only exception, a cello-piano piece where I have the piano on 100% and cello on 80%. I actually wanted to reverse those percentages to have a cello part bigger and piano part smaller, that should be possible, I think?

I now did the Redefine all pages command and redid the page layout, quite a lot of work, but now the file seems to work properly. 

If I understand correctly this problem of file behaving differently in different parts of the piece comes from the fact that I have probably added pages to a document which had a different Page Format and the new pages do not obey the same resize commands?  I need to try and understand this behaviour properly.

… My file is what you called the only exception, a cello-piano piece where I have the piano on 100% and cello on 80%. I actually wanted to reverse those percentages to have a cello part bigger and piano part smaller, that should be possible, I think? …

I would switch to Scroll View, and set the staff size in Scroll View since Scroll View is “page independent” (= for the entire document).

To resize the staves I would use the Resize Tool, and context-click on the staff.

Having a multi-staff instrument (such as Piano) resized to another staff size than 100 % might (or might not) cause problems - with e. g. ledger lines and cross staff notes.

If you are not experiencing problems with the piano’s resized Grand Staff, fine.

But if you experience trouble, consider doing it “the other way around:

Set the Piano’s staff size to 100 %, and the Cello’s staff size to 125 %.

Then, reduce the System Scaling from 100 % to 80 %. (or set the System Scaling to 100 %, and the Page Scaling to 80 %)