I think what happened is that we had a bug so that custom templates did not save any html. We fixed that bug in the core when you brought it our attention.
I just verified that the template form field you use has this code in it:
<field name="study_detailtemplate" type="textarea" rows="10"
cols="100" label="JBS_TPL_DETAILS_STUDY_DETAILTEMPLATE" description="JBS_TPL_DETAILS_TEMPLATECODE_DESC" filter="raw"/>
The "raw" makes it so that html will be passed through. So you should have no worries.
As always, though, I would suggest doing a full site backup with Akeeba Backup prior to installing the new version. You might also backup your JBS tables.
Tom