I think I have found a limit on FemtoIDE which is an issue to me. It appears the maximum number of items you can mark as ‘Copy to SD’ is limited to 256. I have more.
@FManga can this be increased? By an idiot like me??
There isn’t a hard-coded limit in the IDE, other than the size of the SD card image (50mb). I’ve had no problems copying a few thousand files. 
I was receiving an error in FemtoIDE when I had checked ‘copy to SD card’ on more than 250 files. I have since removed the check box and just checked the overall folder and the error has disappeared.
Hmm, it might be a limit on how many files can be opened simultaneously. It’s probably MacOS-specific, then. Can you create an issue on GitHub? I can’t check this right now.
No it definitely happened on both my Mac and Windows machines. I will open a ticket for you but as I found the workaround it is a very low priority.