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Square arrays of sub-micrometer columnar defects in thin YBa$_{2}$Cu$_{3}$O$_{7-\delta}$ (YBCO) films with spacings down to 300 nm have been fabricated by a He ion beam projection technique. Pronounced peaks in the critical current and corresponding minima in the resistance demonstrate the commensurate arrangement of flux quanta with the artificial pinning landscape, despite the strong intrinsic pinning in epitaxial YBCO films. Whereas these vortex matching signatures are exactly at predicted values in field-cooled experiments, they are displaced in zero-field cooled, magnetic-field ramped experiments, conserving the equidistance of the matching peaks and minima. These observations reveal an unconventional critical state in a cuprate superconductor with an artificial, periodic pinning array. The long-term stability of such out-of-equilibrium vortex arrangements paves the way for electronic applications employing fluxons., Comment: 9 pages, 6 figures, to be published in Physical Review Applied