Multi-epoch Chandra X-ray observations of nearby massive early-type galaxies open up the study of an important regime of low-mass X-ray binary (LMXB) behavior -- long term variability. In a companion paper, we report on the detection of 158 X-ray sources down to a detection/completeness limit of 0.6/1.4 x 10^{37} ergs/s using five Chandra observations of NGC 4697, one of the nearest (11.3 Mpc), optically luminous (M_B < -20), elliptical (E6) galaxy. In this paper, we report on the variability of LMXB candidates measured on timescales from seconds to years. At timescales of seconds to hours, we detect five sources with significant variability. Approximately 7% of sources show variability between any two observations, and 16+/-4% of sources do not have a constant luminosity over all five observations. Among variable sources, we identify eleven transient candidates, with which we estimate that if all LMXBs in NGC 4697 are long-term transients then they are on for ~ 100 yr and have a 7% duty cycle. These numbers are consistent with those found for brighter LMXBs in M87 and NGC 1399, which suggests that there does not appear to be a measurable difference between the outburst durations of long-term transient neutron star LMXBs and black hole LMXBs. We discuss in detail a transient supersoft source, whose properties are not easily explained by standard explanations for supersoft sources.
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