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No automatic magic. I duplicate the return, label as Filer, delete spouse info, change whatever is needed (anything marked as J, for example), then do the same for a duplicate return for spouse. I always print first the form MFJ vs MFS to confirm all data is where it belongs and the bottom line is correct. Be sure to note those items which are limited or no allowed for FS, only for joint. It takes a bit of time but less than entering everything from scratch. It does go quicker if you have correctly entered anything that was just F or just S and remember to split those J items, if appropriate. I have done many of these and am grateful for this feature.

My understanding of this situation is that you need to advise your client of the Filing Requirements, Potential Penalties and etc. Ultimately, it's your client decision after you are sure that they understand.

I file a bunch of late 1099s. Especially since I asked them back in January - do you need any 1099s prepared, and they say "no". Then in the midst of July tax prep - there she be - the contractor or self-rental or other NEC that needs filed. So I file it. I'm not the one that's going to be in the wrong!