For the the QIAprep 96 Plus Miniprep Kit or the QIAGEN Plasmid Plus 96 Miniprep Kit, can plates be partially used?
FAQ ID -2319

For the manual procedure, the plates can be partially used. Any unused wells should be sealed with tape. For the BioRobot Universal procedure, the entire 96 sample plate must be used. However, different sized plates may be available from our applications lab.  Please contact QIAGEN Technical Service for more details. 

https://www.qiagen.com/contact/contacttechnicalservice.aspx?WT.svl=m