No, it was only the Westinghouse green R-10 units that remained throughout the calendar year 1989, and were all indeed to have been scheduled to be retired by that year's Labor Day weekend. Of course, the Con Edison asbestos problem a few days later along 8th Avenue in the 50th Street vicinity changed all that. For the record, I made a note in an ERA January 1990 bulletin that during the week ending September 1, 1989, I had observed two 8-car green R-10 consists that were assigned in each evening rush hour, which actual car numbers as documentation.
During the fleet's final summer, I kept a keen eye on the activities of the R-10's on the "C" line, including actually photographing slides of the consists (all green units seen) along 8th Avenue, Liberty Avenue and the Rockaways. During those days of that particular summer I had seen no graffitied General Electric R-10's in use anywhere on that "C" line, but if I did, I would have snapped them on film with my camera, and made a written record of it.
But of course, the September 3, 1989 Con Edison asbestos foulup caused a major headache on the IND, with the reroutes you mentioned in your post. You are correct that some green R-10's were used just oh so briefly durig that mixup, and there is an image of car #2967 at 34th Street-8th Avenue in the R-10 car picture section of this web page, showing as a "C" train ready to leave this interim terminal point back to Rockaway Park.
Keep in mind that I keep a huge back catalogue of E.R.A. New York Division "Bulletins" as far back as 1964, so they are usually as a very reliable reference source in case there is a discrepancy on certain car and route assignment matters, which have been known to come from NYC Transit's roster sheets. The date of November 10, 1988 is the date as written and found in the 1989 "Farewell to the R-10" fantrip brochure for the last date of the graffitied units.
Besides, if there were still to be non-GOH'd GE R-10's in service, let us say, after the December 11, 1988 schedule change with the routes revision connected with the Archer Avenue extension opening, they might to have new roll signs installed all around. This happened on the sister Westinghouse green units, and a good chunk of them from the now 110 car fleet were even seen briefly on the weekend "C" 145-WTC runs on a full time basis until February (or so) 1989.
-William A. Padron
["145 Street, Manhattan...Chambers St-WTC"]