As Linda stated, the FAA (or any other ICAO IR) will not lock-in your ATPL Theory.
You had also better hold off from going down the FAA conversion route.
It appears that, with effect from 17th September 2012, the only credits available towards an EASA Part-FCL IR are the 10 hours you get for holding an EASA Part-FCL CPL (or a Basic Instrument Flight Module Course Completion Certificate).
This is outlined in EASA EU Regulation 1178/2011, Annex I, Sub-Part G and Appendix 6, Paragraph 10.1.
10.1. The holder of a CPL(A) or of a Course Completion Certificate for the Basic Instrument Flight Module may have the total amount of training required in paragraphs 7 or 8 above reduced by 10 hours.
There are NO credits available towards an EASA Part-FCL IR for holding an ICAO IR, unless you hold an ICAO ATPL whereby you can go down the ATPL Validation/Conversion process (providing you meet the criteria for issue of an EASA Part-FCL ATPL).
It is a right can of worms and how this has come about is anybody's guess but essentially the 15 hour ICAO IR conversion process will soon disappear.
We are trying to get to the bottom of this but it does not look promising.
Strike another blow for EASA!
As stated above the best way to get the theory locked in is to do a SEIR before your ATPL theory expires in March 2013, then worry about the conversion later. But to lock the theory you will need to do both the CPL and the IR.
To renew an expired (more than 7 years) IR you need to retake all examinations relevant to the level at which you wish to use the IR, undertake training as required (as determined by the Head of Training at the chosen ATO) and retake the Skills Test.