Hey @knaderi,
I believe your best option is to use Entity/Use Codes for the applicable sales orders from that particular customer. See the following KB articles for more details about Entity/Use Codes:
Partial exemptions for California Tax Connect tax calculations
Exemption Overrides using Entity Use Codes in Tax Connect
Also, I suggest checking out this topic: Avalara and CA Partial Tax on MFG Machinery
Lastly, another option might be this: Create a Single use exemption certificate
Hope this helps!