Hiya, I am one removed my chacra's a few years ago. Had the reinstated by some goddes. Or so I was told. I've written about that here.
I also had a few local clearvoyants take a look at them here

So far I haven't found any ancient literature that describes them. The oldest writings I have managed to track down are from roughly the 1600's AD. Most old religions or alternative/energetic health systems/healing practises I am aware off. Chinese medicine, Ayurveda, Shamanic healing etc. Do not use the 7 or 13 chacra system. In my studies of chinese medicine I was often told that the accupuncture points and meridians have nothing to do with the chakra system.

That said Like slowsnake I haven't seen them in meditations. I have tried to clear them, open them and manipulate them through visualizations etc in an attemt to use them as ascension tools.

In the end I feel that if you feel that working with the chakra's help you in where you want to go. than do so. As with any sympatetic magic or energetic/intentional work if it works it works. I know of people who through the use of inner chakra work have openend the way to abilities and states of mind they probably wouldn't have without the self permission they gave themselves through clearing their chakra's.

I do believe that through the popularization of the chakra idea many usefull ways of regarding them have become more rigid than they may have been in the beginning. This rigidity may be at the root of claiming they were archonic implants. Anyway. Many have removed them and still live.

WIth Love
Eelco