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2

The glyphs are not supported by Libertine in TS1 encoding. Why? I don't know. However in the log file you find Missing character: There is no <B4> in font LinLibertineT-tlf-ts1! Missing character: There is no <80> in font LinLibertineT-tlf-ts1! Missing character: There is no <80> in font LinLibertineT-tlf-ts1! Missing character: There is ...

2

You want to change the digits in math mode: \documentclass[ a4paper, final, 12pt, numbers=noendperiod, BCOR=5.00mm, bibliography=totoc, listof=totoc, headinclude ]{scrreprt} \usepackage[oldstyle]{libertine} \usepackage[scaled=.83]{beramono} \usepackage[libertine]{newtxmath} \usepackage{hyperref} ...

4

You can change all counters using arabic numbers into oldstyle arabic numbers by re-defining the inner macro \@arabic. As well, I provided \Arabic which gives the standard arabic numbering, so for instance, if you wanted enumerate to use standard digits, you can do \renewcommand*\theenumi{\Arabic{enumi}}. However, there is some trouble with page counter and ...

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