There is nothing in the order regarding persons already present in the US.
Other than the Adminstrative parts, there are only a few "bans" in the whole order:
Section 3 (c) - "... pursuant to section 212(f) of the INA, 8 U.S.C. 1182(f), I hereby proclaim that the immigrant and nonimmigrant entry into the United States of aliens from countries referred to in section 217(a)(12) of the INA, 8 U.S.C. 1187(a)(12), would be detrimental to the interests of the United States, and I hereby suspend entry into the United States, as immigrants and nonimmigrants, of such persons for 90 days from the date of this order (excluding those foreign nationals traveling on diplomatic visas, North Atlantic Treaty Organization visas, C-2 visas for travel to the United Nations, and G-1, G-2, G-3, and G-4 visas)." Exceptions are specifically allowed for.
Section 5 (a) "The Secretary of State shall suspend the U.S. Refugee Admissions Program (USRAP) for 120 days."
Section 5 (c) "Pursuant to section 212(f) of the INA, 8 U.S.C. 1182(f), I hereby proclaim that the entry of nationals of Syria as refugees is detrimental to the interests of the United States and thus suspend any such entry until such time as I have determined that sufficient changes have been made to the USRAP to ensure that admission of Syrian refugees is consistent with the national interest."
Section 5 (d) "Pursuant to section 212(f) of the INA, 8 U.S.C. 1182(f), I hereby proclaim that the entry of more than 50,000 refugees in fiscal year 2017 would be detrimental to the interests of the United States, and thus suspend any such entry until such time as I determine that additional admissions would be in the national interest."
Section 5(e) actually allows for exceptions.
In each and every case it bars ENTRY. Anyone already IN the US is NOT covered under the EO - IOW, these people will not lose any "right" they already possess. If they leave the country and want to return, then they are subject to the new rules.
What?
What harm could only 1,000 of these folks per state DO??
Which means they are covered by it.