We need more info.

What are your program settings in Preferences - Edit, in the pane “Automatic Settings”?

I have not exactly this:  Preferences - Edit, in the pane “Automatic Settings”, but Automatically Constrain Dragging, is that what you mean. This is Unchecked.

What program are you using?

I suspect that you are not using the “full Finale”, but rather one of its smaller sibling - perhaps PrintMusic, or SongWriter.

No, the full version, Final 25.5.0.259.
But - sorry - I looked the wrong place - under Preferences> Edit I find Automatic Update Layout and Automatic Music Spacing and more.
If I uncheck both, the manual vertical changes will be retained, but only until I select Music Spacing - the manual positions will disappear.
I'm sitting with a big score with some manual positionings, and if I want to make Music Spacing, all of them disappear. Then I have to wait until the piece is completely finished before making manual positionings, and it is not so realistic.

In Document Options>Music Spacing, check Incorporate Manual Spacing (not Clear Manual Spacing), then respace the music. Your manual adjustments will be preserved. 

There is a third option, Incorporate, but it is either broken, or nobody knows what it does.

I have tried both Incorporate and Ignore Manual Spacing, but not with the wanted result. When I respace music, the manual spacings will be removed. Sorry.

Looking at Finale Help, it seems that Finale should take into account manual adjustments or not when calculating the Music Spacing:

Manual Positioning: Clear • Ignore • Incorporate. Manual positioning refers to any manual dragging you’ve done with the Speedy Entry tool or the Special Tools Tool. Choose Clear from the drop-down list to remove all manual adjustments while spacing the music. Choose Ignore from the drop-down list to have Finale space the music as if it weren’t manually positioned; after spacing, Finale adds the positioning to its result. Finally, choose Incorporate to include any manual adjustments into Finale’s calculations while spacing the music.

… Finale 25.5.0.259.
But - sorry - I looked the wrong place - under Preferences> Edit I find Automatic Update Layout and Automatic Music Spacing and more.
If I uncheck both, the manual vertical changes will be retained …

I suggest that you keep Automatic Update Layout selected, and only de-select Automatic Music Spacing.

When you have Automatic Update Layout selected, you can trust that What You See, Is What You Get (WYSIWYG).

You do not have to, always Apply Music Spacing to the entire document.

Instead, you can select only the region you need to re-space.

Then, only the selected region will be affected.

Thank You, Peter, for the good advices. I'll do so.

Regards Jørgen

It's always a good idea to develop a good workflow. Enter notes, articulations, smart shapes, expressions and, if applicable, lyrics, and only then work on layout and manual adjustments. Doing this final step too early is like painting a house before the walls have been put up. And ALWAYS leave Automatic Update Layout ON!