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Good question. If you plan on simply using your custom software within your organization, there shouldn't be any problem. If, however, you plan on selling or distributing your software outside of your organization, I would recommend that you talk to the SolidWorks Partner Program about this. Note this clause of the EULA in Section 3:
You may not use the Software or the Documentation to develop application(s) for distribution to third parties unless you are a member in good standing of the SolidWorks Partner Program or have entered into an agreement with DS SolidWorks for such usage/distribution.
If you think this applies to you, contact the Partner Program about becoming a partner. I can personally attest to the excellence of SolidWorks' partner program. Unlike other CAD software partner programs, you don't have to pay a fee to join and you might qualify for complimentary licenses for development.
I met a company who have solid works license . They design their product on solid works. They do same think many times.And i guess i can do their design by using c# with api under their licence (is it possible). However i did not know that it is necessarily to apply solid works partner program.So which one I should get in this link Partner Product Program | SOLIDWORKS level1, level2 and level3 .
So basically you would be paid (as a sub-contractor) for the time spent creating a program for one company.
Unless you intend to sell that same program to other companies, I don't believe the EULA statement applies.