This is a known issue and has been around for a long time (since 7.5, maybe?). The problem is that Paratext does not see new files added by a user without some other change. The cause of this is some caching done when determining what changed for S/R. Basically, without having opening of the S/R dialog take much longer (one or two seconds per project), it can’t detect new files in a project.
When Paratext creates a new file, it is able to update the cache so it will be S/R’d, but when a user adds a new file, Paratext has no way to know that it now exists without the aforementioned slowdown when doing a S/R.