I have an IBM Notes Java agent that posts fields from 50,000 Notes documents to a website containing a PHP file. The agent performs a single post per document. Eventually, the PHP file processes these documents.
However, after a few thousand documents, IBM Notes crashes. I couldn't find any relevant information in the log file. Is there a limitation with Notes that prevents it from handling this volume of documents?
You're probably missing at least one required call to the recycle() method of some of the objects you're using. See here.
And also consider switching to use the OpenNTF Domino API instead. (Actually, I think the github home for it is better for you to check out than the OpenNTF site.) One of the improvements it makes over the standard API from IBM is that it handles the recycling for you, so you won't have problems with running out of that pesky back-end storage allocated by the Notes C API underneath the Java layer.