It is not advisable to alter anything within an Enterprise Miner project's directory structure. Altering even one file could potentially render the project unusable. Instead, I'd suggest determining why the project has grown large and using appropriate mitigations. See this section of the documentation about planning disk space: https://go.documentation.sas.com/doc/en/emref/15.2/n1xnqglvjt8k9fn1cx4eotahcmnk.htm#p1qrvx4asabvh0n1...
There are ways to "back-up" a diagram using a model package (there are some caveats) and then removing that diagram, in the processing freeing up the space that diagram is using within the project directory. Please consider talking to SAs Technical Support before doing this so that you are aware of the pros and cons and caveats of this method.
