I don’t believe it will affect your engraving or cutting using the original nozzle or the air pump nozzle. However, when using the nozzle with an air assist, you should replace the power adapter that came with the air assist accessories. The 60 W adapter cannot handle the power if you are operating your iEngrave with an air assist. You may need to contact support to send you the appropriate adapter with your air assist.
On the other hand, have you tried operating your laser using the IdeaStudio on your desktop? You might want to try it first to determine if this is a software issue or the unit itself. In addition, the SD card should be inserted in the SD slot in your machine all the time.