Many functions use the Check Database function to determine whether the database is consistent. Often editing an inconsistent database can yield more and more inconsistencies. However it is sometimes useful to use such an editing function in the process of fixing the database. In such cases, the "Ignore check database" toggle should be set.
An example of the use is for the Break Contig function. If we find that a database is inconsistent due there being a gap in the contig, the obvious solution is to fix this using Break Contig. But Break Contig checks for consistency, and refuses to work if the database is inconsistent.