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It seems the number of countable words in a selection is a proportion of the total number of words in a file. In a file of 3,083,437 words I was able to have a selection with 1,694,545 words counted. Then in a much smaller file with 507,375 words I was able to have a selection with just over 100,004...

Does unchecking "Load file Importers in the background after Nisus Writer Starts" (from NWP Preferences:Advanced), resolve this issue? (Then relaunch NWP).
We have seen this issue before:
http://nisus.com/forum/viewtopic.php?f=18&t=6175

It is true, the knob is quite slippery; anyway try this: Quit Nisus Thesaurus if it is running. Then, from your Home Library/Containers/com.nisus.NisusThesaurus/Data/Library/Saved Application State/com.nisus.NisusThesaurus.savedState (Folder), delete the files: data.data window_1.data window_2.data ...

You have to drag down the dot between the search box and the definition box:

In Bibliography Options in the Format Manager for APA 7th, check the Case options; it may be that the drop-down menu is at "small CAPS":

Here is how my APA 7th appears:

What format is applied to the bibliography?

I agree this is undesirable.
I had made a feature request for this Find option. I have Jedit Ω which has the option to not share Find strings with other apps:

You can find Nisus macros here:
https://nisus.com/pro/macros/

Nisus Writer Pro version 3.1:
Changed: jumping to a note reference should place the insertion point after the reference, not select it entirely.

You can use this online PDF to PDF/A Converter:
https://www.pdftron.com/pdf-tools/pdfa-converter/
1. Select the type of PDF/A from the drop-down menu
2. Upload your PDF file.
3. Download PDF/A of the file.

If you still have Wintext app on Classic MacOs, you can salvage the text as explained in this post:
https://nisus.com/forum/viewtopic.php?p=17932#p17932

From System Preferences:Keyboard, tab to Text and uncheck “Correct spelling automatically”.

What you describe can only happen when a left-to-right script language paragraph style is applied to the selected text.
To overcome the problem, the paragraph style applied should have at least "Language: Arabic" attribute:

If the text is entirely in Arabic script, is Arabic language applied to the paragraph style (from the flag menu in the Stausbar)?
Are you working with a text which was copy-pasted from another source?
Is another script direction involved?