I am looking into a similar issue and wanted to highlight this older thread, which suggests that transferring Citi points into the "donor" EVA Air account, then transferring all those miles together into the "recipient" EVA Air account. Those miles will be kept separate from any miles in the "recipient" EVA Air's account.

EVA Points Transfer

In the older thread there are claims that the Citi points transfer can occur within just 2 days but there are also some frustrating stories about it taking many phone calls and even 2 weeks.