You're not parsing the sentence correctly.
is the subject of .
is the object of .
In , modifies , not .
**** means "thought ~~ and started" or "started, thinking ~~". "Started to think" would be .
You can parse it this way:
>
≂
(The has replaced/absorbed the . is the topic/theme of the sentence, so it's marked with the and moved to the front.)
"JR Eastern Japan thought that [the number of] working people would become insufficient in the future and started researching automatic trains." / "JR Eastern Japan started researching automatic trains, thinking they would become short of workers in the future."