I had a 2TB external volume, connected via Thunderbolt, which was almost full - there being a handful of MB remaining - around eight I think. Somehow the previously-existing (and searchable) index on there was wiped out - the (hidden) folder ".Spotlight-V100" existing but the sub-folder Store-V2 containing nothing - that, I believe, containing the indexes. Quite how this came about I don't know but I'd be surprised if it were simply as I rammed it. (I've also filled my boot volume in recent days whilst rendering a video file - not good as it does all sorts of weird things like resets one's wallpaper and Notifications settings - though not every time as I know from hitting this more than once.) I followed the official advice on fixing this issue but to no avail. After adding the volume to "Privacy" as described in there I manually deleted the parent folder - i.e. ".Spotlight-V100" - and on removing it from "Privacy" the folder re-appeared, with its sub-folders but, again, Store-V2 was empty. Only after making a bit more space available (1 GB) was the index rebuilt - i.e. Store-V2 was populated - and so Spotlight searches worked again. I know space is required for the index though it didn't take up more than was originally free on the drive - i.e. when down to a handful of MB - so maybe it needed more, as workspace, to generate the index. I've suggested Apple improve their help page to cover this requirement.
OS X 10.11.1.
Edited by Harry_The_Bustard, 21 November 2015 - 04:28 PM.