resolve as By Design
Make the file names unique. Skyline only starts adding # suffixes when the resulting replicate names will not be unique.
You can also change these default names in two ways:
1. Edit > Manage Results - then double-click on a replicate you want to rename, or select it and click the Rename button.
2. In the Document Grid, create a report/view with "Replicate Name" as a field. This is an editable field, and allows you to rename in bulk with copy-paste or type in names more quickly and press Enter to commit the change.
We need to have some way to disambiguate duplicate names, similar to what Windows Explorer does when you try to rename a file to an existing name.