It is important to understand the difference between burning a CD using Nero with and without INCD.
Think of a DVD as a library of books with an index showing book locations. If you wanted to stop somebody finding the book, then you could simply remove the entry in the index. The book would still be on a shelf somewhere, and the only way to find it would be to manually search the library.
In the same way, if you delete a file from a DVD, you only remove the index but the file is still on the disk.
However, in a library, you could delete the index and physically remove the book to reclaim the space held by the book. This is what INCD does for you. The file space is reclaimed and can be re-written.
The key point to understand is that the filing system with INCD is more complex, and is less compatible with other PCs and is reported by some people to be less reliable. The more simpler (ISO) DVD filing system (non-INCD) is compatible with virtually all PCS and is very reliable.
So extra flexibility (i.e. ability to remove files and reclaim space) comes at a price. I (personally) would advise against INCD if you are using it for critical data (e.g. backups).
It is not much of a problem to copy all files from a standard ISO DVD to a hard disk and reburn accordingly.