Reorder a Master List Based on a Reordered Subset
Retina 0.8.2, 51 bytes

+`(\b(\w+),(\w+)\b.*¶.*\b)\3,(.*\b\2\b)
$1$4,$3
1A`


Try it online! Takes input as a comma-separated list of subwords on the first line and a comma-separated master list of words on the second line. Explanation:

(\b(\w+),(\w+)\b.*¶.*\b)\3,(.*\b\2\b)


Find two adjacent subwords where the second word precedes the first on the master list.

$1$4,$3


Move the second word to appear after the first word in the master list.

+`


Repeat until no words appear out of order.

1A`


Delete the subwords.