A complicated question about LiFePO4 batteries, - and switching.

Another question regarding the above battery type! There are variety of techniques used when switching between batteries - on/off/on switches, good switches with a cut out between the movement, two batteries with a diode to prevent flow between both batteries, etc.
The question I have concerns an older glider with limited battery space (Libelle), previously using SLA batteries and and a simple switch between the two. I will be upgrading with a new panel, likely LiFe batteries and want a back-up as well. While I understand the function of the diodes in the switching circuit, is there any reason to be concerned about their use with the LiPo battery and the internal Battery Management System? Imagine two LiFePO4 batteries that have equal charges, only one is discharging at a time until some threshold is reached and they switch over as determined by diodes outside the internal battery system. Is there a reason to question this type of circuit with the use of this new battery technology and the Battery Management System within?
While I love these new batteries, I don't want to bring on any new problem in the air, being quite aware that the wiring is only to contain smoke.

Thanks ahead, Mark