There were not thousands of F-1 engines manufactured. There were a bit over a hundred manufactured between flight and test models.
The whole "we can't make them anymore" meme has a tiny kernel of truth but it's been blown way out of proportion the more it's been repeated.
When the F-1 was manufactured a lot of the actual assembly of parts was done by hand. That meant Rocketdyne's engineers and machinists had a lot of tribal knowledge that was lightly or partially documented at best or not documented at worst. NASA and Rocketdyne maintained all of the designs and documentation and knew everyone involved in the engine manufacturing.
In the early 90s a lot of these Rocketdyne people were interviewed [0] and asked to review F-1 manufacturing techniques as part of the Space Exploration Initiative [1]. Restarting production of the F-1 would have been practical but more expensive than the alternate plan to go with an SSME derivative.
While the F-1 is an impressive engine it has downsides. It's enormous and heavy. The Saturn V's first stage (S-1C) was 10m in diameter while the Space Shuttle's external tank was 8.4m in diameter. The Shuttle's ET was going to be the core of the proposed SEI rocket (and SLS). With a 8.4m tank diameter it would be more difficult to mount more than two F-1s.
With only two engines it would be more dangerous of a vehicle for manned missions as a flame out in one engine could be disastrous. It would also make it more difficult to throttle the engines for different launch profiles. Moving to a larger core would have required all new manufacturing infrastructure, flight qualification, and unknown follow-on issues.
Tl;dr The F-1 was an awesome engine but not perfect or even desirable for all purposes and the "we can't build them" meme is stupid.
[0] https://www.thespacereview.com/article/3724/1
[1] https://en.m.wikipedia.org/wiki/Space_Exploration_Initiative