But of course employer can file the I-140 on your behalf with you being temporarily out of the country. The L-1A visa is a "dual purpose " visa. You will still be welcomed back into the country on your still valid L-1A visa.
Kindly be advised that the answer above is only general in nature cannot be construed as legal advice, given that not enough facts are known. It is your responsibility to retain a lawyer to analyze the facts specific to your particular situation in order to give you specific advice. Specific answers will require cognizance of all pertinent facts about your case. Any answers offered on Avvo are of a general nature only, and are not meant to create an attorney-client relationship.
There should not be a big concern in this matter.
My answers are for general information only, NOT A legal advice because these are not tailored to your specific situation. Contact an Immigration Attorney if you need legal advice.