In our microfabrication lab, we get messages to work with photoresists and e-beam resists (generally PMMA) in different work stations, because 'they can contaminate each other'. What is the reason for this, if it is indeed problematic?
They are known to interact chemically. For example, in case you spin coat PMMA in a spin coater that was not cleaned after the previous use with photoresist (or vice versa), the resulting deposition onto the coater walls becomes hardly soluble in aceton. This layer then may generate excessive particles during subsequent removal.
In case both PMMA and photoresist intrude into the vacuum part of the system, there is an increased risk of blocking it. Also there might be other associated problems.
To sum up, it's definetely better to avoid using these two substances together on the same work station. In case only one station is available, always thoroughly clean it before switching from photo- to ebeam-resist and vice versa.