bullhead to flatbottom

Of course there are no flatbottom chairlock points so where flatbottom rail is fitted bullhead has to remain in place for the chairlock units. Ealing common is a good place to see it, right outside the IMR. replacing the chairlocks with flatbottom 4' points or another type is a very expensive exercise. Other than that I don't think there is anything too special about replacing bullhead with flatbottom in tunnels or anywhere else. Generally it's much the same as a good old tunnel recon job as once done night after night by the P-Way recon gangs.

As for joining rail there are are 'lift' fishplates to join rail different types and to account for wear in like types.

There's a difference between rerailing and reconditioning, shifting from bullhead to flatbottom in tunnels is generally going to be reconditioning i.e. ballast removal, gunning out of the old trackbed, new trackbed concrete and drainage, new concrete sleepers. Rerailing is more about changing like for like so typically replacing or transposing rails, changing the odd railchair, perhaps repositioning railchairs to get better purchase and sometimes replacing a worn timber in extreme cases.
Of course everything wears in the tunnel over time and when I began my LT career reconditioning in the tunnels was like painting the forth bridge, a never ending renewal process across the deep level tube. Of course there would always be a signals presence on hand to take possession on the section being renewed and to remake the track connections, repack trainstops to suit the new gauge etc. I never worked on a recon job personally but I worked in and around them at times during resignalling works on the Northern line in the 1970s and jobs such as assisting the P-Way Chief Inspector (basically carrying a Tilley lamp to illuminate whatever he wanted to see) walking through recon sites and through the two halves of the associated ballast train to get from one end of the site to the other.

The last replacement of bullhead with flatbottom that I saw was at Earls Court Picc when I had to deal with a few signal maintenance issues. AFAIR it was all new sleepers, I'm really not sure what preparations were undertaken to lay them as I saw only the last night of the job and as the last few Pandrol clips were being knocked in but it all looked very new and I expect it was a full recon job but that was about 10 years ago IIRC. Techniques and working methods have moved on so much, you don't tend to see gangs of P-Way shouldering baskets of ballast out of the tunnels anymore, the privateers that do large track renewals are very machine minded and there is a lot less manual graft than there used to be.

AFAIK LUL/Metronet/Tube Lines still do small rerailing jobs and I worked on lots of those on the Picc transposing rails, renewing rails, renewing stocks & switches and rail crossings in the late 1990s and until 2001. Lots of measuring, remeasuring and cutting, rail pulling etc before I could rebond the affected track circuits and test the signalling. This was all pretty much manual graft in the same old tradition with some mechanical aids to carry rails, more modern drilling machines instead of the old hand operated 'bikes' etc and some mechanical saws too although they were difficult to use in some tunnels and often failed before doing the job.

No doubt things have moved on even more since I last worked in a tunnel 10 years ago.

I don't think it's that big of an operation, what is a bigger operation in tunnels is the change of wooden sleepers to conrete ones.

At Bank they've replaced the track and put in new wooden sleepers (Which I thought was quite odd), but the ride is still uncomfortable because of the sleepers. If they ever bother to put in Concrete sleepers then hopefully the ride will become smoother an bit more quieter...

There are some videos of track replacement on YouTube on the Central Line, have a look.

So why would they, eg re-rail chunks of the nothern line (charing X branch) with bullhead, when they knocked out the [whatever the rail fixings were sitting on] and replaced/reinstalled then...