Does this problem also occur with 2.0? Does it also occur in ordinary saving? Can you share the file?

The issue occurred with PDFBox 3.0.0, and I haven't tested it with 2.X.X. In fact, the PDF is encrypted and doesn't allow editing. I'm sorry, but for certain reasons, I can't provide the PDF file.

I had a look at 2.0, one of the changes isn't needed (2.0 doesn't use computeIfAbsent because it doesn't exist in the jdk, and also avoids using a null, so maybe this was introduced in refactoring), the other ones are. Your changes look useful so I'll commit them next week to give time for other opinions (COSWriter is a difficult class). I'll also add some logging.

We have to ensure that the resulting pdf isn't (more) corrupt that the origin one if indirect object references are omitted. To remove a reference from a COSArray shouldn't be a big problem (the object reference is simply missing) but to remove a reference from a COSDictionary without removing the key will lead to a corrupt pdf In such cases the key should be removed as well or the corrupt reference should be replaced by a COSNull object

In that case I'd really like to test this with a file. I forgot to mention yesterday that I tried to modify a PDF by "blanking" an object and then load and call saveIncremental() but no problem occured.

I thought the issue was caused by document encryption, but after a simple test, I discovered it was not the case. The document seems to have been generated using iText 5.5.8.

0003719771 00000 n 
0003759924 00000 n 
trailer
<</Info 5 0 R/Encrypt 7894 0 R/ID [<e3d8be7479575ba4b5622d7b671d2255><64acf33dec0b965797b470cbf8346962>]/Root 75 0 R/Size 7895>>
%iText-5.5.8
startxref
3760055
%%EOF

perhaps the original document had already lost the obj references.

maybe remove lost obj reference from a COSArray is good idea.

https://issues.apache.org/jira/browse/PDFBOX-5717 is the same problem

Please test whether your code works with the recent changes by @lehmi with the latest snapshot build:
https://repository.apache.org/content/groups/snapshots/org/apache/pdfbox/pdfbox-app/3.0.2-SNAPSHOT/