Account transfers can be processed with margin loans as long as the account is projected to remain margin compliant post-transfer. When you initiate an online application, you will be prompted at the conclusion to specify how you intend to fund the account. If your account is held with a U.S. broker, then you can authorize a full or partial ACATS transfer which will be initiated once your account is approved.
If you select a full account transfer, your broker will send a list of securities held along with cash (debit or credit ) balance. IBKR will perform a credit check and if it passes the transfer will be accepted. If you select a partial account transfer, you will be prompted to enter the position and cash balances you intend to transfer and a credit check will be performed shortly thereafter.