My team produces packages, comprising frontal material and appendices. A few months ago, I developed a style guide, template, and customized the styles to use in both the front material and appendices. We lock the template, but unlock those areas we deem editable. The problem occurs when we work with Appendix A. App A is dynamic, meaning that each package has customized information. Further, information for App A is from an unknown source document.

Major Problems:
1. When users import App A directly into our template, even the locked front material changes formatting. Example: 1.0 becomes A; 2.1 becomes (A). 2.1.1 becomes 1.1.1.1.1.1 
The first list item "a." indents approximately 4 inches.
We still need to format App A.

2. We have isolated App A by turning off formatting from App A and then importing from the source document. Everything looks fine, even when we save a document. When we close the document and reopen, the "Major Problem 1" occurs.

3. We formatted the source document to better support our template. (Refer to #2 above.)

The only solution thus far is to copy from the source document and import it as Text Only into App A of the Template.  The front material retains its formatting, but App A loses any formatting we may have previously performed, goes into default formats, and our users spend hours fixing problems.

Does anyone have experience of developing customized styles and templates, and working with source documents?