Tips for working with sequences:
Make sure each sequence is it's unique folder.
If you loose a link then choose reload footage. If that doesn't work, choose replace footage.
Keep the numbering system simple and short. Scene_A100_Take_2_00001.tif is barely acceptable. Scene A Take 2 01.tif is going to give you problems. Scene A Shot 1.tif isn't going to work at all.
What numbering system do you use? AE has always preferred sequences with padded numbers, not Maya's default unpadded numbering or even the old *.number.extension scheme it inheritetd from its IRIX days... And Rick has a point about using spaces vs. underscores, too. Not sure about having everything in separate folders. The days where operating systems would get to their knees with more than 500 files in a folder are long over and as long as there are distinct prefixes/ suffixes in the name, AE is perfectly able to keep everything straight.
I am using the "name.#.ext" format. They are all in separate folders. I keep the names super simple with no extra dashes, spaces. Do you think it's possibly the "." rather then dashes? I know MAYA is super picky about it being a "." rather then a dash in the naming convention, maybe AE needs it the other way. I will also try the padding next time as well, noticed the files were not.
Like I said before, they always come in fine, they just randomly lose connection here and there....Thanks guys.