Until very recently CFE were expanding with bigger aircraft and the airport wanted to make best use of peak slots which meant forcing out the smaller players via prohibitive pricing. This is the same GIP who pulled an identical stunt on flybe and Air Southwest at LGW.
What has changed at LCY in terms of Skywork is twofold. Firstly they also fly the larger DHC8-Q402 and secondly, the number two operator at LCY, CityJet, looks very vulnerable to closure.
Hence they now have a more pressing need. It would be a complete about turn for Loganair to do this, they're not known to be bold, that's why they're still around!