I think this problem is cuased by the wrong partition configuration, please follow below steps to correct it(please note that the ubuntu image on emmc will be damaged):
After the u-boot prompt “BPI-R2>” appears, please enter the command “emmc ecsd” to check partition configuration, on your board, the partition configuration should be 0h
[EXT_CSD] Partition config : 0h
Then run command “emmc pconf 0x48” to change it
Power off this board, remove SD card, and then power it on, the board will boot with lede test image which is stored in EMMC.
The ubuntu system you programmed to EMMC has been damaged yet, need to re-program it, so sorry for this.