I am working on SD cards and mostly using SdFat.h library. However, I would need some functions from SD.h, I am getting some errors when compiling. Is there a solution for solving this incompatibility between these libraries.

At the moment, I need to have the available size left on SD card. I know how to do it in SD.h but not in SDFat.h

If you mean file.available(), SdFat does not provide available() since this function does not always provide the correct result in SD.h. The problem is available() is declared as an int in the Stream class. Type int is limited to 32767 bytes but files can be much larger, up to 4294967295 bytes.