I know this is an old issue but this can still happen to unfortunate souls today. This used to happen to me until one day Android Studio showed a pop-up saying something along the lines of "You started Android Studio from a bash script, run the binary directly for better performance." So, having seen this pop-up, instead of running studio.sh that comes bundled alongside the binary on modern distributions of AS, the next time I ran the binary /bin/studio directly and it didn't do all this indexing stuff. It seems that the bash script to start AS also disregards the index cache that is usually created.

TLDR: If you're running the bash script studio.sh to start AS, try instead using studio binary and see if this helps.