Yes, you should put 3.5kV AC from pri to sec and , less than a certain current should flow...i think its a mA or so, over one second.
The standard isolation test for production is to put 500V AC from pri to sec, for one second, and m,easure the current, it shoudl be less than 250uA.
As Penfold implies,. you never do the 3.5KV AC test on a unit that will be sold after production, because it would be weakened by that test. The unit that gets that test, will get thrown away.
To test for general safety, you need to be at least mains peak in your DC voltage........but even thats not enough, because the mains suffers transients up to 10kV and beyond, so your supply must offer some safety from that.....is there such thing as a totally safe SMPS outh there, that would be safe against loads of repeated 6kV transients?......probably not, they all would eventually break down and become unsafe, but i guess there is always this trade off beteeen safety and cost.
I mean, your protection against a tranisnet is usually a MOV......and they break down and die after a certain number of transients.