I've sent an email about this question to the jPSXdec team.
I'm also thinking that maybe I should put make a request for a decompressor/compressor at the lab 313 team, I took a quick glance at their forums, they kind of made one specifically for the Front Mission 2 team, a project my co-founder is also part of (a web manager AFAIK). It's worth a try, they seem to be really helpful with this kind of thing.
Let's wait for now and see what happens, I'll post here as soon as I have new information. I've halted editing for now until we can overcome these latest obstacles.
UPDATE: a guy from jPSXdec answered my email and said their program isn't able to do what I wanted (replace entire blocks of an iso image) but there may be one that can do it, he wasn't able to name one though. After a few days wait my post at lab313 hasn't gotten more than a few views and no replies.
I'll contact esperknight to see if he can help us out.