Yes,Text flow is different in QuarkXPress AppStudio project and in QuarkCopyDesk Article

The typographic features of QuarkXPress AppStudio project and Quark CopyDesk article are not same.

So in order to keep consistency in text flow when the article is assigned from QuarkXPress, please make the following changes in AppStudio project:

  1. Update all the Paragraph StyleSheets with 'No Hyphenation' which means, edit the Paragraph StyleSheet, (Edit Paragraph StyleSheet window opens). Navigate to Format tab, select 'No Hyphenation' under H&J dropdown.

  2. Do not use Open Type Styles. To know about this, edit any of the Character Style Sheet and make sure all the styles along with asterisk* sign should not be applied on text along with All Caps style also. User can convert the text to Upper and lower case using Style > Change Case options

  3. When AppProject is open, navigate to Preferences (Edit > Preferences on windows or QuarkXPress menu > Preferences on Mac) > Project > General and uncheck the option 'Use OpenType Kerning' on right hand side.

Make the above mentioned changes in any of your AppStudio project and then assign the article from the same. In QuarkCopyDesk also please make sure user should not apply Open Type Styles on the text.