We present a two-epoch Sloan Digital Sky Survey and Gemini/GMOS+William Herschel Telescope/ISIS variability study of 50 broad absorption line quasars of redshift range 1.9 < z < 4.2, containing 38 Si IV and 59 C IV BALs and spanning rest-frame time intervals of approximately 10 months to 3.7 years. We find that 35/50 quasars exhibit one or more variable BALs, with 58% of Si IV and 46% of C IV BALs showing variability across the entire sample. On average, Si IV BALs show larger fractional change in BAL pseudo equivalent width than C IV BALs, as referenced to an unabsorbed continuum+emission-line spectrum constructed using non-negative matrix factorisation. No correlation is found between BAL variability and quasar luminosity, suggesting that ionizing continuum changes do not play a significant role in BAL variability (assuming the gas is in photoionization equilibrium with the ionizing continuum). A subset of 14 quasars have one variable BAL from each of Si IV and C IV with significant overlap in velocity space and for which variations are in the same sense (strengthening or weakening) and which appear to be correlated (98% confidence). We find examples of both appearing and disappearing BALs in weaker/shallower lines with disappearance rates of 2.3% for C IV and 5.3% for Si IV, suggesting average lifetimes of 142 and 43 years respectively. We identify 5 objects in which the BAL is coincident with the broad emission-line, but appears to cover only the continuum source. Assuming a clumpy inhomogeneous absorber model and a typical size for the continuum source, we infer a maximum cloud radius of 10^13 to 10^14 cm, assuming Eddington limited accretion.
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