Background of this scenario:
http://www.ingber-aronson.com/archive/H1B concerns.html
http://www.vkblaw.com/news/threehundredseventyeight.htm
This case may or may not be a violation of H1B status. Most of the people (more than 90%) on H1B were/are in this situation but USCIS generally ignores this scenario except very very few officers (and that too recently I guess). With regards to replying to the RFE I would suggest these possible explanations/options for particular scenarios.
1. If your permanent labor certification (NOT A SUBSTITUTION, you should be direct beneficiary of LC) was filed before April 30th 2001, claim 245(i) section by paying $1000.00 with I-485A Supplement and provide explanation saying you were unaware of the H1-B LCA obligations (explanation not a must coz ignorance of law is not an excuse) and you should be fine.
2. If you were issued a visa at a consulate outside the country after January 2001 and entered into the US before filing I-485, explain in detail saying you maintained valid status after your last lawful entry and provide paystubs, w-2, tax returns etc and I-94 copy.
3. LCA violation may not be your violation but your employer's if any. Also here is the excerpt from AILA's letter to INS "For these reasons, the employers had no alternative but to file the initial petitions under their own addresses. The question then becomes whether the employers were under an obligation to file an amended petition. The answer is clearly no. INS has historically tied any obligation to amend a petition to add a new work site to the necessity for a new labor condition application under Department of Labor rules.[1] The Department of Labor’s “temporary placement time limit” rules were invalidated in 1996 under the NAM decision, leaving no requirement for a new labor condition application when an employee is assigned to a temporary work site. Thus, under long-standing INS policy, no amended petitions were required. "
The temporary placement rules that require new LCAs were struck down by the court in a case NAM v. Reich in 1996 coz of lack of proper request for comments and review. Ordered the Section 735(b)(4) (20 C.F.R. Sec. 655.735(b)(4)) invalid and void.
Here is the link for court order.
http://www.visalaw.com/docs/namdol.html
After reviewing the court order the DOL-ETA finally issued a iterim rule, requesting comments on 12/20/2000. The short term placement rules for H1-B dependent employers and willful violators for H1-B worker placed at a worksite not covered by LCA became effective only from January 19, 2001 (section 755.735). For more details here is the link.
http://frwebgate.access.gpo.gov/cgi-bin/getdoc.cgi?dbname=2000_register&docid=page+80209-80254
for the complete regulation here is the link.see under Employment And Training Administration
http://www.access.gpo.gov/su_docs/fedreg/a001220c.html
By the above analysis it makes sense to say that it was lawful to work in a area not covered by the LCA for longer period BEFORE January 19, 2001.
Discuss these options and others to overcome this with your attorney as he knows your case more than any of us.. These are my opinions, do consult your attorney and better consult other attorneys too.
Also post your complete case details