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You always will have the jsp in the folder shared/elements /<asset>. It is independent from the csdt.
If you try to export just one missing template you will have most information about the sync problem. Could you share here the logs error after the sync problem?
One thing that I have seen (and it has confused some of our developers) is that the template is going to be found in CSDT element view nested under the Site that the template is assigned to - so if you have A site it will be seen under A/assettype/templatename
but if you have 2 sites (A/B) and the template is shared to BOTH (note: note ALL) it will be found under A/assettype/templatenmae AND B/assettype/templatename --
NOW for the part that trips folks up: if the template is shared to ALL - it will show up under a NEW node called All Sites so you will find the template under: @All Sites/assettype/templatename but you will NOT find it under the A/B nodes -
Asset to site mapping is kept in the AssetPublication Table.
If you look at this table you will see that there is at least one entry per asset in this table (the publication id will be the site that you created the asset in). As you share to specific sites there will be an additional row added with the publication id for each addtional site. If you do a Share to All those rows will be removed and replaced with the 'magic' publication id "0"