Hello Jordi,
Could you let me know which MCU and debugger are you using?
For example, if you're using an LPC you could try using Flash Magic to flash the binary through ISP.
Or If you are using a Segger debugger there's options like the J-Flash for J-Link Pro and better version, and if you have a J-link base or EDU version you could try using the command console to download your program.
Also I found strange that you could not use the Program flash action in MCUXpresso. Could you try using the Clean up Debug first before using the program flash:

Let me know if this helps you.
Best Regards,
Alexis Andalon