I have hacked out a Visual Basic Script which will do this but I will not finalize it or post it yet because I do not know if you are happy with a command line solution:
File1
Comment: 0,0:00:00.00,0:00:00.00,Default,,0,0,0,,Only this words must be replaced with line in text2.
Dialogue: 0,0:03:27.77,0:03:28.91,Alfa,,0,0,0,,These are the words in the second line that must be replaced.
Dialogue: 0,0:08:12.62,0:08:13.87,Example,,0,0,0,,And goes on.
Dialogue: 0,0:09:27.77,0:09:28.91,Rotate,,0,0,0,,These are the words in the second line that must be replaced.
Dialogue: 0,0:10:12.62,0:10:13.87,Elefante,,0,0,0,,And goes on.
Dialogue: 0,0:12:27.77,0:12:28.91,Catalunya,,0,0,0,,These are the words in the second line that must be replaced.
Dialogue: 0,0:13:12.62,0:13:13.87,Perro,,0,0,0,,And goes on.
File2
Pellentesque nunc augue, mattis vitae rhoncus pharetra, convallis sit amet
lorem. Suspendisse ac arcu erat. Suspendisse euismod mi vel sem porttitor et
interdum nisl auctor. Mauris cursus, neque nec hendrerit faucibus, elit velit
pharetra elit, quis accumsan odio purus eget neque. Aliquam hendrerit tempor
tortor eget ullamcorper. Nulla est leo, elementum vitae aliquam vel, porta
faucibus libero. Sed eget est ut turpis fermentum sagittis. Maecenas
sollicitudin sem a tortor interdum bibendum. Morbi vel purus erat. Suspendisse
Output
Comment: 0,0:00:00.00,0:00:00.00,Default,,0,0,0,,Pellentesque nunc augue, mattis vitae rhoncus pharetra, convallis sit amet
Dialogue: 0,0:03:27.77,0:03:28.91,Alfa,,0,0,0,,lorem. Suspendisse ac arcu erat. Suspendisse euismod mi vel sem porttitor et
Dialogue: 0,0:08:12.62,0:08:13.87,Example,,0,0,0,,interdum nisl auctor. Mauris cursus, neque nec hendrerit faucibus, elit velit
Dialogue: 0,0:09:27.77,0:09:28.91,Rotate,,0,0,0,,pharetra elit, quis accumsan odio purus eget neque. Aliquam hendrerit tempor
Dialogue: 0,0:10:12.62,0:10:13.87,Elefante,,0,0,0,,tortor eget ullamcorper. Nulla est leo, elementum vitae aliquam vel, porta
Dialogue: 0,0:12:27.77,0:12:28.91,Catalunya,,0,0,0,,faucibus libero. Sed eget est ut turpis fermentum sagittis. Maecenas
Dialogue: 0,0:13:12.62,0:13:13.87,Perro,,0,0,0,,sollicitudin sem a tortor interdum bibendum. Morbi vel purus erat. Suspendisse