Well it appears I was selecting columns that were nor ints and my long table included elements that had not been converted. I changed the original solution to parse to Int all non-already-int columns only, with an addition to the one line solution:
transform!(df, names(df, r"numbers").=> ByRow(x -> typeof(x)!=Int ? parse(Int,replace(coalesce(x, "0"), "," => "")) : x), renamecols=false)