The problem with the cloner is actually a problem with the ATA5577 chip.. it does not support tear protection, which is a way of ensuring the data you want to write to a memory block or blocks is not "torn" half way through a write operation. Just like if your computer is busy writing data to the hard drive in your computer and the power goes out mid-way through, you will have a corrupt file... if data is being written to the ATA5577 chip and the magnetic coupling is not good enough, the write operation may require more power than is available and you will get a torn write, corrupting the data. If the data being written is the ID number data, then your tag will not be readable by an HID or EM reader, however you should still be able to attempt a re-write and make it work. If, however, the corruption occurred during the configuration of the ATA5577's analog operation, then the tag might not be able to properly communicate anymore because it's analog operation (the way the chip communicates over the magnetic coupling) could now be "out of spec" to the point that even a cloner can't talk to it anymore.
Because of this, any cloner could cause the same issue at any time. The best way to ensure it won't happen is to use a device that has a well designed antenna that can couple really well with the cylindrical antenna in the xEM. So far we have not found anything that is guaranteed to work well, so we are not offering a cloner at this time. Others have tried using the Proxmark with some success, so if you have the money, it might be a good idea to use that.