Per Rand al'Thor♦'s answer below, the site manager for Chakoteya.net is apparently unwilling or unable to make changes at their end to resolve this problem.
That being the case, our options are now limited to trying to convince an SE Programmer to make the changes en-masse or making the changes ourselves.
Sometime over the past few days, Chakoteya.net appear have changed the URLs of their episode transcripts, enforcing case and rendering the links broken.
http://www.chakoteya.net/nextgen/132.htm = No longer working
http://www.chakoteya.net/NextGen/132.htm = Working.
http://www.chakoteya.net/ds9/447.htm = No longer working
http://www.chakoteya.net/DS9/447.htm = Working
http://www.chakoteya.net/doctorwho/32-12.htm = No Longer working
http://www.chakoteya.net/DoctorWho/32-12.htm = Working
http://www.chakoteya.net/voyager/718.htm = No Longer working
http://www.chakoteya.net/Voyager/718.htm = Working
http://www.chakoteya.net/startrek/16.htm = No Longer working
http://www.chakoteya.net/StarTrek/16.htm = Working
A quick search indicates that some 445+ answers possibly now have broken or invalid links, although the actual number is probably lower given that several will have already been fixed or will link to sources that are unaffected.
Obviously we could go through and just change all of those that are affected but this would engulf the front page. Does anyone have any better ideas?