This work reports the discovery of cycle-to-cycle modulated spectral line and atmospheric velocity gradient variability in long-period Cepheids based on 925 high-resolution optical spectra of $\ell$ Carinae (P $\sim$ 35.5 d) recorded during three heavy duty-cycle monitoring campaigns (in 2014, 2015, and 2016). Spectral line variability is investigated via cross-correlation functions (CCFs) computed using three sets of spectral lines (weak, solar, strong). A metallic line velocity gradient, {\delta}v$_r$ (t), is computed as the difference between weak and strong-line RVs. CCF shape indicators BIS (asymmetry), FWHM, and depth all exhibit clear phase-dependent variability patterns that differ from one pulsation cycle to the next. Weak-line CCFs exhibit these effects more clearly than strong-line CCFs. BIS exhibits the most peculiar modulated variability and can be used to identify the presence of cycle-to-cycle modulated line profile variations. {\delta}v$_r$ (t) clearly exhibits cycle-to-cycle differences that correlate very closely with modulated BIS variability, suggesting perturbations of the atmospheric velocity field as the cause for modulated spectral line variability. These perturbations are most significant during contraction and are not in phase with the pulsation, transmitting information between consecutive pulsation cycles. This work shows RV curve modulation to be a consequence of atmospheric velocity gradient perturbations. Possible origins of these perturbations and their impact on Cepheid RV measurements as well as the projection factor used in Baade-Wesselink-type distance determinations are discussed.
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