Can CNN autoencoders have different input and output dimensions?
Auto-encoder (AE) is an architecture that tries to encode your image into a lower-dimensional representation by learning to reconstruct the data from such representation simultaniously. Therefore AE rely on a unsupervised (don't need labels) data that is used both as an input and as the target (used in the loss).
You can try using a U-net based architecture for your usecase. A U-net would forward intermediate data representations to later layers of the network which should assist with faster learning/mapping of the inputs into a new domain..
You can also experiment with a simple architecture containing a few ResNet blocks without any downsampling layers, which might or might not be enough for your use-case.
If you want to dig a little deeper you can look into Disco-GAN and related methods.They explicitly try to map image into a new domain while maintaining image information.
I am working on a problem which requires me to build a deep learning model that based on certain input image it has to output another image. It is worth noting that these two images are conceptually related but they don't have the same dimensions. 
At first I thought that a classical CNN with a final dense layer whose argument is the multiplication of the height and width of the output image would suit this case, but when training it was giving strange figures such as accuracy of 0. 
While looking for some answers on the Internet I discovered the concepts of CNN autoencoders and I was wondering if this approach could help me solve my problem. Among all the examples I saw, the input and output of an autoencoder had the same size and dimensions. 
At this point I wanted to ask if there was a type of CNN autoencoders that produce an output image that has different dimension compared to input image.