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I did the same (installed alloytech templates, removed the whole bin folder, installed nuget package), but I have 440.0 everywhere - dlls, web.config, nuget package. Did you remove bin prior to installing nugets?
No, but I did now and it still downloads 394.2 instead of 440.0. I dont use the Alloy temmplate though.
-Edit: Just tried to update on a similar site and it works to update there. Weird.
I installed the 7.5.394.2 CMS version with deployment center. Today I added the nuget package(and set the download nuget packages to true). However, it says 7.5.440.0 in nuget.packages and web.config for all references but the references downloaded are 7.5.394.2. I confirmed this by removing and addind the nuget package (making sure all files are removed and downloaded). Changing all "440.0" to "394.2" in web.config makes it run again.