Your ResNet might still work, if you retrain it, but might waste the feature extraction layers, as your encoder might have already created valid features.
I don’t know what shape the output of the encoder would have, but if it’s not an image tensor, the first convolutions in your ResNet might not be the best choice, as their input might not contain any spatial pattern.
However, as always, you shouldn’t let these assumptions stop you from running some experiments and report your findings.