I have only been able to get one program uploaded to my D1 mini, so I am not experienced.
in my hours of trying to find how to create a BLINK program, I finally succeeded.
in my reading, when you create the project, the plaftormio creates a unique name and then uses that for the file.
seems the need to offer the user to create a variable to name the file, then use that for the rest of their needs. (not the user needs)
what I read is that when PIO creates the file structure, it create fixed references to the file name and they are placed in multiple places in the newly created set of files.
in the end, renaming a folder in the OS is like renaming a library. all external and internal references become invalid.
so, until the coders of this software get to some simple and elegant way to show a name you want to see that makes sense to you vs. a file name that makes sense to them, you are going to have to put in good notes on the top of your programs.
=================== EDIT ============
go in your OS to the folded with the name you want to change
copy the folder and paste it with a new name or paste it and re-name it.
open ATOM / ProjectIO
select 'open project'
now click that little check mark in the left column
the project io system will do it's thing and create all the correct links for this new folder name.
delete your old folder.
it is a bit of a work around, but in the end, you get what you want.
create a new project, nothing but setup and void
in your OS copy that folder to a new folder and name it
open it and then click that checkmark for a build. should be 100%
once you have that, it should be in the file system and you can copy your file into the new project.
do not copy your job into it before running the BUILD