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The Eckhaus instability is a secondary instability of nonlinear spatiotemporal patterns in which high-wavenumber periodic solutions become unstable against small-wavenumber perturbations. We show in this letter that this instability can take place in Kerr combs generated with ultra-high $Q$ whispering-gallery mode resonators. In our experiment, sub-critical Turing patterns (rolls) undergo Eckhaus instabilities upon changes in the laser detuning leading to cracking patterns with long-lived transients. In the spectral domain, this results in a metastable Kerr comb dynamics with a timescale that can be larger than one minute. This ultra-slow timescale is at least seven orders of magnitude larger than the intracavity photon lifetime, and is in sharp contrast with all the transient behaviors reported so far in cavity nonlinear optics, that are typically only few photon lifetimes long (i.e., in the ps range). We show that this phenomenology is well explained by the Lugiato-Lefever model, as the result of an Eckhaus instability. Our theoretical analysis is found to be in excellent agreement with the experimental measurements.