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.
Sola lingua bona est lingua mortua
ἡ μόνη ἀγαθὴ γλῶσσα γλῶσσα νεκρὰ ἐστιν
lišanu ēdēnitu damqitu lišanu mītu
"Du stammst vom Herrn Adam und der Herrin Eva ab", sagte Aslan. "Und das ist zugleich Ehre genug, um das Häupt des ärmsten Bettlers zu erheben, und genug, um die Schultern des größten Kaisers auf Erden zu beugen. Sei zufrieden." Aslan, Die Chroniken von Narnia, Prinz Kaspian von Narnia. CS Lewis. Übersetzt von Wolfgang Holbein und Christian Rendel.
Accordance Configurations :
Mac : 2009 27" iMac Windows : HP 4540s laptop
Intel Core Duo Intel i5 Ivy Bridge
12GB RAM 8GB RAM
Accordance 11.2.4 and 12 Accordance 11.1.6 and 12
OSX 10.11 (Yosemite) Win 10 Professional x64