Large list items are not crawling

Recently we have migrated SharePoint 2007 application to SharePoint 2013. In that we are having a list which contains 40000+ items and each item have unique permissions set based on the business requirement.
After migration, we have ran full crawl on the web application. After the crawl, the list items are not crawled and displayed in the search results. When checked in the crawl log, there is no entry related to the list items.
Based on suggestions from the blog and microsoft we have changed the FilterProcessMemoryQuota and DedicatedFilterProcessMemoryQuota to 500 MB from 100 MB.
Still, the items are not crawled. Later we have modified some of the items in the list and ran the incremental crawl. The list items which are modified are crawled and available in the search results.
We have scheduled the incremental crawl to run on every night and full crawl to run every week end (saturday) night. What happened is the incremental crawl that run after full crawl deletes all the items which are modified and crawled before the full crawl
with a message "Deleted by the gatherer ( This item was deleted because its parent was deleted. )". This happens only with the incremental crawl run after the full crawl, but the subsequent incremental crawls add the items to the
search results until full crawl run.
Please advise on this.
Ramkumar

40k items with individual permissions? That's going to have significant performance impact across your content database and is getting close to the hard limit(?) of 50k scopes per list http://technet.microsoft.com/en-us/library/gg128955(v=office.15).aspx
Having said that...
Your full crawl is picking up the items but the first incremental crawl is subsequently deleting them. Are you really using Incremental crawl or is this continuous crawling? Are all list items being deleted or merely some of them?
I'd normally put this down to the crawler not being able to identify the items, which may be the case here, but this sounds a little more interesting.

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