Updating a modified image file across entities using it
The image width and height are stored in the field tables (field_data_FIELD_NAME/field_revision_FIELD_NAME), in the FIELD_NAME_height and FIELD_NAME_width columns.

If you know the file id (fid) of the file you need to change the data for, and the width and height of your new image, you can just run the following queries against the database:

UPDATE field_data_FIELD_NAME 
SET FIELD_NAME_width = WIDTH, FIELD_NAME_HEIGHT = HEIGHT
WHERE FIELD_NAME_fid = FID

UPDATE field_revision_FIELD_NAME 
SET FIELD_NAME_width = WIDTH, FIELD_NAME_HEIGHT = HEIGHT
WHERE FIELD_NAME_fid = FID