I have never claimed to be an expert when it comes to dealing with 'under the bonnet' motoring but, based upon personal experience, another cause could be a duff HT lead. It could mean that you're running on four cylinders for some of the time but only on three cylinders at other times.
In terms of costs:
A blocked fuel line shouldn't really cost anything to fix. The garage should be able to clear it simply by blasting some compressed air through it. (Once again, that's based upon personal experience, rather than any expert knowledge).
I wouldn't expect a Citroen fuel filter to cost a great deal but, as the former owner of a BX, I'm aware that Citroen don't always design their cars with 'ease of access' for mechanics in mind. i.e. the labour costs might be far greater than the cost of the filter.
I've not had an HT lead replaced recently but, as far as I recall, its not particularly expensive.
Chris
PS: Just another thought. I've also experienced some intermittent 'loss of power' problems, in the past, because of a blocked air filter. This was actually the result of a small oil leak. (The oil had soaked into the air filter). So, even though you state that the air filter has been changed fairly recently, it's worth checking again. (Air filters are among the cheapest spares for any car).