On project builder, uploading a file with the "TI File(s)" button seen here:
disables the options for pausing/resuming, resetting, uploading any other files or uploading any ROM files, until the file transfer is complete.
On the other hand, leaving the tab pauses the simulation, of which you have to click the resume button to resume the emulation again. Unfortunately, leaving the tab while the file transfers pauses the simulation, and disables the option to resume it, making the screen permanently frozen (until you refresh the tab), which looks like this:
As you can see in the above screenshot, you are not able to click the "Resume" button (as it is greyed out), which pretty much bricks the emulation until you refresh the page (which, can delete any progress or files you put on the emulator).