The old, but still widely-used, legacy AXT Arabic fonts were designed before 2006, when QuarkXPress, with version 7, began to support Unicode.
The font names of all legacy AXT Arabic fonts begin with the prefix AXT, and if you open them in the Character Selection Dialog, then you will see that all Arabic characters are located in the Latin Basic and Latin Supplement 1 code pages.
This means that legacy AXT Arabic fonts cannot be used to also display non-Arabic text, which can be a problem if you want to design a bilingual diary (for example English-Arabic) and need the fonts for both English and Arabic to look the same. If multilingual font homogeneity is important, then you should use Unicode-encoded Arabic fonts.
If you change the font of some text in a QuarkXPress file, then if the new font does not support all the ligatures of the previous font (not usually an issue when moving from one AXT font to another), or if one font is AXT legacy and the other is Unicode-encoded, then you will need to re-process that Arabic text.