It should not, provided you maintain all your banking records that reflect all of your business transactions. When you say "we are a sole proprietor," and "we have a business checking account," that implies that you are not a sole proprietor. A sole proprietor is one individual, hence the title "sole." Rather, it could be that you are partners in a partnership. A partnership requires at least two persons, and a partnership does not require any formal agreement between the partners (although, depending on the nature of the business, it may be prudent to have a formal written agreement) and further, does not require a filing with the appropriate state agency in order to establish its existence.
If you have a partnership, then the transfer of money out of your business account into a personal account, may have tax implications; however, it does not by itself raise any red flags. Moreover, if you determine that no such partnership exists, and you are a sole proprietor, then the same applies, namely, there may be some tax implications associated with winding down some aspect of your business, but these are ordinary business transactions, and by themselves do not raise any red flags.
@Lara
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