Baryon Acoustic Oscillation (BAO) surveys will be a leading method for addressing the dark energy challenge in the next decade. We explore in detail the effect of allowing for small amplitude admixtures of general isocurvature perturbations in addition to the dominant adiabatic mode. We find that non-adiabatic initial conditions leave the sound speed unchanged but instead excite different harmonics. These harmonics couple differently to Silk damping, altering the form and evolution of acoustic waves in the baryon-photon fluid prior to decoupling. This modifies not only the scale on which the sound waves imprint onto the baryon distribution, which is used as the standard ruler in BAO surveys, but also the shape, width and height of the BAO peak. We discuss these effects in detail and show how more general initial conditions impact our interpretation of cosmological data in dark energy studies. We find that the inclusion of these additional isocurvature modes leads to a decrease in the Dark Energy Task Force figure of merit (FoM) by 46% i.e., FoMISO = 0.54 × FoMAD and 53% for the BOSS and ADEPT experiments respectively when considered in conjunction with PLANK data. We also show that the incorrect assumption of adiabaticity has the potential to bias our estimates of the dark energy parameters by 2.7σ (2.2σ) for a single correlated isocurvature mode (CDM isocurvature), and up to 4.9σ (5.7σ) for three correlated isocurvature modes in the case of the BOSS (ADEPT) experiment. We find that the use of the large scale structure data in conjunction with CMB data improves our ability to measure the contributions of different modes to the initial conditions by as much as 95% for certain modes in the fully correlated case.