That solves it, but we can speed up the build farm from being “aware” of the new .ino file by making a small change in the file and then compiling (insert a blank line anywhere!). The changed file gets properly saved and then it can compile immediately.
Thanks @ScruffR I was going a little crazy about this issue. Possibly this issue can be tweaked on Particle’s side. The “Use This Example” button may not be fully initializing all variables, or the file is being saved too early and just re-save the file or save the file at the end of the process.
The easiest solution is probably something like
printf "\n " >> filename.ino
In linux that would add a new line to the end of the file.