For Lin's story it is telling me to get human supplies kit etc. but that was done long ago and Android's story is completed on this file. Is there any way to fix this short of starting a new file?
That shouldn't be possible without cheating or editing the code. To fix this, you're going to need to reverse those cheats or edits, or load to a time before they were applied. Otherwise you may have to restart the game because things are out of sync.
