Thanks for the sample files.
After an initial test, I am able to reproduce the following two issues as you described:
CELLSNET-45280 - Sparklines disappear after re-saving the file
CELLSNET-45281 - Sparklines disappear after rendering to PDF
I used the following sample with your template XLSB file:
Workbook workbook = new Workbook(strFilePath);
Our product team will evaluate your issues soon. Once we have an update on any of the issues, we will let you know here.