See other postings on this blog for a refresher of these rules:
403(b) Retirement Distributed as Housing Allowance
Caution is advised when comingling non-church [401(k)] and church [403(b)] accounts. The church monies may become ineligible for a housing allowance designation if careful records are not kept of the 401(k) roll over amount (and subsequent earnings on that amount) versus church and minister 403(b) contributions and related earnings. The minister may be called upon to defend his calculations of tax-free housing related to his 403(b) portion of the church plan account.
We do not have definitive guidance on this particular matter. Accordingly, we recommend avoiding comingling monies from a 401(k) rollover with monies that can be distributed tax free through a housing allowance designation from a 403(b) account.