There's a very good reason for it all...
Each time a new route is loaded into the system the people in scheduling allocate flight numbers for a particular route. These people are not concerned with callsigns...their only aim is to maximise use of the aircraft.
The route starts operating and the flightplans are filed accordingly. The callsigns will be the same as the flightplans.
If it turns out that a particular flight is operating at the same time as another with a similar callsign then most likely ATC will ask for it to be changed. They do this in a number of ways such as contacting the operations dept directly or by asking the flight crew to advise operations of the similarity.
The callsign is then changed to something different.
So take the example of RYR9911 becoming RYR99TR and RYR9912 becoming RYR35LK.
It is most likely that operations were made aware of RYR9911 having a similar callsign to another flight for example on 1st September so the flightplans are changed to a new callsign. Then the schedule changes at the end of october and it turns out that RYR9912 now has a similar callsign to some other flight so that gets changed too. They dont necessarily look at the outbound callsign to get ideas for the inbound. In addition the other flight could have a callsign also beginning with the numbers 99 so it gets changed to something totally different.
The callsigns used are mostly random however it is also quite common for the person doing the refiling to use their initials in the latter part of the callsign. They also use the last two letters of the aircraft operating the flight on the day that they are asked to refile. It is very possible that EIDLK was operating RYR9912 when the callsign was changed to RYR35LK.
In other cases they simply reverse the callsign. An example is RYR552 DUB-MAN is RYR5WT and on the way back to DUB as RYR553 it's RYR5TW...these would most likely have been changed on the same day.
Another example of this is when aircraft are being delivered from boeing the callsign is always RYR800 followed by the last letter of the aircraft registration. ie EIEBF would be RYR800F and EIEBG would be RYR800G.
I hope this goes some way to answering your question.