The final advice from The Ins and Outs of Caulking deals with flashing. Modern sealants are capable of impressive performance in controlled laboratory testing and also in well-executed joints on buildings. As indicated previously, however, sealant joints in residential construction are usually executed by individuals with limited training and cannot be expected to function indefinitely. Sealant joint failure can occur without obvious indication.
Sealant joints should thus not be considered as acceptable substitutes for formed metal flashing. Well-executed formed metal flashing makes use of an exceptionally dependable force of nature: gravity. Water management by drainage is a time-proven strategy in the construction of wood buildings. For example, at horizontal joints in plywood panel siding, metal Z-flashing or shingle-lap joints are effective; sealant joints are not an acceptable substitute. Where there are drainage paths, it is important that caulk, if used, not block them.
Remember, good caulking can protect your doors and windows if applied properly. This report, available free for download on the FPL website, can tell you all you need to know.