Instead of using the replace function to add the title, create the title using paragraph, perform the proper styling, then use "replace" to add it to the title of the slide.
For example, here we make the slideTitle blue and size 10, and THEN add it to the title section of the slide.
pre = Presentation('Test');
slide = add(pre, 'Title and Content');
slideTitle = Paragraph('Test title');
slideTitle.FontColor = 'blue'
slideTitle.FontSize = '10'
contents = find(slide,'Title');
replace(contents(1),slideTitle);
Best Answer
This is expected behavior. An enhancement request has been submitted to allow formatting content when Slide Master content has been deleted.
Workarounds
The current workaround is to create a new Slide Master (without deleting its content) and recreate the Slide Layouts you need from scratch in the new Slide Master.