If the little remains of OTL Langobardic are a taste on what influence Upper Bavarian would get, then I don't think that it would be so weird. Probably would have it's own taste distinct from core Bavarian and Alemannic, but still Upper German.Yeah. The Lingua Franca is Latin as IOTL and there isn't any kind of "official language" enforced from above to marginalise local languages (that's a much more modern invention in most cases), so people speak whatever language or dialect they've always spoken, while then also knowing Latin to communicate. Geographically the majority langauge would be a derivation of Frankish, so closer to Dutch than modern German, while eastern and southern Germany speak more or less the same as what they did IOTL. The territory of Austria is different from OTL though, with the Lombardic influence creating a dialect that'd probably sound very weird to speakers of OTL German.
Except if Lombard itself is more like the OTL Romance language.