Phil,
The IsDeleted attribute is a 'soft' delete. It doesn't detect if a module has been discarded.
The Last Modified On date will detect when the package was changed. I just put a module on a page and then deleted it to see what would happen in Modules. Since the Created On and Modified On mean just that, not Deleted On, the Modules table won't record that history.
I know of one way you could get the info you need. It's involved SQL writing but should work. The last time I did anything with this was in Advanced TSQL classes some time back.
There are tables that record what transactions have happened when there are updates, deletions, additions to tables in TSQL. This is where you would have to get the information, I think. The reference is TSQL Fundamentals by Itzik Ben Gan. My copy is for SQL Server 2008. Because what was done with the data once committed, rolled back, etc. is recorded in transaction logs, you should be able to get the data there.
If I recall right, you'd have to go through backups, if you have them and compare them. That is, get a date range of what happened when and if you have full and incremental backups in that time frame you *should* be able to get what was deleted, updated, added from Modules and Module Definitions from the transaction logs. This is how a restore can happen -- the logs are a record of exactly what happened and when.
If the logs don't exist there isn't a way you could do this.
My answer is a bit vague, I know. I just tried to find in the book where this was but could not.
-- Update, found this on Google: https://logicalread.com/sql-server-dbcc-log-command-tl01/#.WVqxnYjyuiM. This will get you on the right road but TAKE HEED to the warning -- executing the function dbLog with production data is at your own risk. There are exercises in Itzik's books that you can get up to speed on against test data instances. You'd have to monitor tables like Tabs, Tab Modules, Modules, Module Definitions, etc. to track what's happened and when.
My word to the wise -- fly anything you're going to do by a DBA and get their blessings first.
Wish I could help more.
Best,
Mike Durthaler