@C_G_Hemmingsen
You say you are familiar with the pitfalls of working with linked structures in Project but it sounds like your customer is not. For review, when working with linked structures in Project, none of the files should ever be renamed, moved, overwritten or "saved off" to another location. Ideally all the files in the structure should be located in a single directory on a local drive and not be operated over a network.
You also indicate the customer has inter-project links and a resource pool file. That increases the link complexity and ups the ante for corruption. My guess is your customer either saved one or more of the files off to another location, perhaps thinking having a backup was a good idea (it is not in this case), or added/deleted subprojects or inter-project links without doing so properly. Incomplete link changes will result in link fragments (i.e. corruption) and can produce strange results like you report.
As far as tools to identify Project link structure problems, I don't know of any but you might find some with an internet search. I wrote a macro that converts a dynamically linked master/subproject structure with inter-project links into a "flat" file with inter-project links converted to normal predecessors/successors. Part of the conversion process includes file integrity checks prior to and during conversion. However, the macro is not freeware. If you are interested let me know. Otherwise I suggest you set aside a weekend for that massive manual rebuild and also "school" your customer in the rules for working with linked structures in Project.
John
