Some application systems (e.g., medical imaging, research data) accumulate files in forward-marching manner, as in creating new timestamp directories for the chronological storage of data. Those provide the opportunity to formulate Excludes to avoid rescanning directories previously treated for incremental backup, thus limiting the view to new areas of the file system so as to minimize work.
I don't know if Tivoli Continuous Data Protection for Files might be applicable to this environment: worth a review, as it works with the OS to treat new data. If no ready solution, the overall issue may need to be brought to the fore with the vendor and application owner as untenable as it has been proceeding. In cases like this, a solid definition of backup/recovery needs is called for, both in terms of application needs and any legal requirements. Sometimes, just a solid mirroring of data is all that is needed. The vendor contract may have to be reviewed to see what remedies may be available, if there no good solutions are apparent, and the vendor is unhelpful. Richard Sims
