As others have suggested, there is a slight issue here with the assumption that suffixed routes must have a "parent", i.e. are a variant or deviation, and not that they may be suffixed to show some other information, e.g. clockwise and anti-clockwise circulars, serving two locations from the same core route, or to convey come other information. There may have been a "parent" at some point, but that was removed for whatever reason and the suffix has remained to avoid a double renumbering (e.g. you wouldn't want to withdraw the 1, and then immediately renumber the 1A to 1, lest passengers think it is still the old 1).
The classic example that comes to mind is the (former?) West Midlands use of 'E', which I believe stood for 'Exception', to denote a short working. Brighton & Hove seem to be adopting X for "not serving all stops", except on the regency routes, where the routes along Lewes Road are limited stop, and the 29X is an even-more direct version for a few journeys.
1st Bus Stop have the 418R (but no 418 route).
Red Route Buses have the 418W (but no 418 route).
This is the odd pair. As far as I can tell, they operate over the same route. Indeed, Redroute had both until the end of the last school year. There was a 418 route a long time ago, though. I wonder whether the 'R' was once "Relief" (see below), but then can't explain how W came along (they both serve Wrotham school), unless they did operate over a different route at some point.
Arriva Kent have the 77X (but no 77 route).
They used to, though - it is now run by Nu-Venture. In any case, I think the usage here stems from the corridor, where a 77n number is used for a stream of services coming from Tunbridge Wells schools to West Malling and Kings Hill (771-776 are all used, in one direction or another). Kent started to renumber/alphanumerize a number of school routes before Covid to fit corridors, in much the same way the 600-series is used in Medway.
Brookline Coaches have the 4A (but no 4 route).
They did until July. The contract for the 4 passed to Hams Travel, but Brookline retained the 4A, which runs through to/from the 67. The 4 requires a DD, but the 4A/67 an SD, so there was no real need to change that number "just because".
Compass Bus have the 35A and 35C (but no 35 or 35B routes).
Compass Bus have the 66A and 66C (but no 66 or 66B routes).
In both cases for clockwise-anti-clockwise.
Hams Travel have the 5C (but no 5 or 5A or 5B routes).
I believe the C here is for Cranbrook (the school it serves), as a wide variant of Arriva service 5.
Nu Venture have the 3A and 3C (but no 3 or 3B routes).
Another case where they now stand for Anti-clockwise and Clockwise. I believe there was a plan for a 3B variant, but was dropped for simplification.
Stagecoach South East have the 3A (but no 3 route).
As others have said, they used to. But as it is only a minor variant, there was no need to renumber it (especially if there were ever any plans to re-increase the frequency by reintroducing the 3).
Not quite in the spirit of the original question, but Arriva Kent & Surrey also have the 6H, which shows short workings of the 6 between Tunbridge Wells and Tunbridge Wells Town Centre, and Nu-Venture have started the 588R, which is for "Relief" to the main 588... call it a different number and scholars don't get on it, give it a suffix and they do... This is all similar to Bus Vannin's lettering, (e.g. J for Jurby, F for Foxholes).
Edit: Forgot to add Travelmasters. Their system largely consists of a core number for the schools they serve (e.g. all 370s go to one school, all 371s to another), but with a wild array of suffixes to show route variations. There are a substantial number of Sheppey - Sittingbourne buses over a variety of routes, and doing it this way saves needing about 20 route numbers). This does see a variety of otherwise unusual suffixes, e.g. Q for via Queenborough, or W for to West Minster.