I would try to look for patterns in what you are doing when it fails.
I would also examine the differences between this tool and any other user tool you have. Is it the biggest, is it in some way unique ? Also, is this tool constantly growing or do you delete stuff from it ?
Basically you are looking to turn an intermittently reproducible bug into a 100% reproducible one. At that point its much easier to see what's going on. Of course I'm assuming its a bug and not something more mundane like intermittently running out of disk space or some such thing.
Earlier in this thread I made some comments concerning temporary file use. I don't know if those comments apply in your case. Take a look.
Finally when Accordance crashes do you get a crash report and stack trace anywhere ? That would be a big help.
When you say "after doing a number of updates" do have a feel for how many and whether its consistently the same number ?
It might be worth someone else importing the tool and seeing if they can repro. the problem. I'm not sure how much the file might compress oh and I don't know if it refers to lots of whizzy modules or not. I have comparatively few modules and almost no commentaries so I don't know if bad links would cause an issue. I could give it a try if you can get me the tool file. BTW, that makes me wonder something - are all the links in the file ok ?
Also what version of 10.x are you on ? I'm on 10.1.7.
Accordance Configurations :
Mac : 2009 27" iMac Windows : HP 4540s laptop
Intel Core Duo Intel i5 Ivy Bridge
12GB RAM 8GB RAM
Accordance 10.3.4 Accordance 10.4.0pr1 and Aleph 10.4.0b1
OSX 10.9 (Mavericks) Win 7 Professional x64 SP1