If I understand you correctly you plan on upgrading both your CPU and mobo from an APU/FM2+ setup to a CPU/FX setup.
This can be done pretty easily if you follow a few key pointers.
1. FX does not have any M-ITX mobos available but FM2+ does so make sure that your case is compatible.
2. If your OS is the OEM version you will have to re-purchase your OS.
3. You will loose PCIe 3.0 lanes. The Fx line only supports PCIe 2.0
4. You may loose SATA 3/6 Gb/s There are few FX boards that support SATA 3