We propose a convolutional recurrent autoencoder (CRAE) to compensate for time mismatches in a photonic analog-to-digital converter (PADC). In contrast of other neural networks, the proposed CRAE is generalized to untrained mismatches and untrained category of signals while remaining robust to system states. We train the CRAE using mismatched linear frequency modulated (LFM) signals with mismatches of 35 ps and 57 ps under one system state. It can effectively compensate for mismatches of both LFM and Costas frequency modulated signals with mismatches ranging from 35 ps to 137 ps under another system state. When the spur-free dynamic range (SFDR) of the unpowered PADC decreases from 10.2 dBc to -3.0 dBc, the SFDR of the CRAE-powered PADC is over 31.6 dBc.