In fact, it is not a problem having a mixed environment with 568A and 568B pinouts if you do not mix different pinouts in one cabling channel. The only possible difficulty is additional administration burden for you.
At this time, the current cabling standard TIA/EIA-568A supports 568A pinout as standard and 568B as optional.
As a conclusion, I would recommend migrating to one pinout scheme (568A or 568B) based on your current situation. If you have more channels with 568A, then migrate to 568A. If you have more channels with 568B, then migrate to 568B.
Roman Kitaev, RCDD