A single member LLC is a disregarded entity, so depending on how things are titled will depend on whether or not this will work.I've seen @Dave Foster weigh in on this topic in the past, so hopefully he can pop in here and let you know.

However, the rule is actually that you must correct the calculations in the year the error was discovered.So advocating a willful blindness to the depreciation during ownership is one of the best ways for your client to end up with "willful disregard" penalties as well as a fat preparer penalty.Run from this person. 

If anyone tells you that, disregard everything else they have to say as well.

Single owner LLCs are disregarded for tax purposes so everything flows to the owner of the LLC.

Cost segregation applies to the owner of the property, which is a disregarded LLC, which is the same as you personally - assuming your description is accurate.

My question is - can I maintain all records and books and file taxes at the parent company level and treat my individual LLCs are disregarded entities?

It’s what they call a disregarded entity. 

Or since I have it in writing saying no partial payments are allowed will the court disregard their partial payment?

@Javier GaillardFor US federal income taxes, the partnerhip and the disregarded entity LLCs are tax neutral.  

If you choose to disregard it, it's incumbent upon you to validate your own theories, instead of relying on others to do it for you.