Dear list members,

It was pointed out to me on the BVP list by the author of the श्रीमल्ललितालालितः website:

That just means that the writing of a repeating word/phrase was skipped by the scribe. In most cases it is already known by the reader or already written once before by the scribe.
So, if it is nyAsa prakaraNa, then शिख शिर etc. mean शिखायै वौषट् शिरसे स्वाहा etc. If it was done with the mantra, then it is assumed by the scribe that the reader/practitioner known the mantra owing to his study of veda-s. And so on.

Also Charles DiSimone noted:

In older brahmic manuscripts produced throughout Greater Gandhāra these dots are commonly used similarly to danda. They are referred to as dot like punctuation (although they are not always used as punctuation!). Maybe something similar going on here?

Also the correct link to the manuscript is:

https://archive.org/download/AgyanDhvantaDeepikaShriSomnath4966Alm22Shlf4DevanagariTantra_201708/Agyan%20Dhvanta%20Deepika%20-%20Shri%20Somnath_4966_Alm_22_Shlf_4_Devanagari-%20Tantra.pdf