After upgrading to 3.4.13 our config files no longer retain their encoding after transformation using “Detect from template”.
In the attached file Web.config has utf-8 encoding while License.config has ISO-8859-1, which they both need to keep. However, after substituting the variables both of the encoding for both files has changed. Additionally we cannot select “utf-8” or “ISO-8859-1” as the output file encoding because they both need to keep their original encodings.
I am having difficulty reproducing the issue you are seeing. If I substitute variables in files with different encodings their encodings are preserved.
Would it be possible to get a copy of your package or config files?
Also, do you know what version you upgraded to 3.4.13 from to help narrow down any changes that might be causing this?