Are there any examples of now completely landlocked former river mouths or estuaries that became so after continental collision? As an example, consider the closure of the ocean between India and the Eurasian Plate – is there any evidence today, e.g. up in the Himalayas, of ancient river mouths or estuaries that are now stranded on the convergent boundary of the two continents? As a corollary are there any rivers today which contain evidence of an opposite flow direction in the past, as a consequence of the above? Such cases, if they exist, would be interesting mirrors to the idea of continental rifting's contribution to river flow reversal (I'm thinking of the extraordinary discovery of the River Amazon's former east-to-west flow before South America rifted away from Africa: http://www.livescience.com/4253-amazon-river-flowed-ancient-times.html).
There were certainly river mouths or estuaries in the rivers that drained off the proto-Himalayas into the last retreating stages of the Neo-Tethys Ocean. Such rivers comprised dozens of small rivers and the westward-flowing Proto-Ganges itself, which deposited the Siwalik formation which now forms the Lesser Himalayas. That is, the southernmost 'soft' 'salt and pepper' sandstones, up to about 2500 metres , which now abut the Indian plain. However, there is almost nothing left in terms of recognizable estuarine sedimentary structures. It has all been compressed, folded, imbricated, overthrust and subject to varying degrees of diagenesis and cataclasis. Most of this sediment was meandering mud flats, sandy outwash and restricted shallow marine sediments, with some similarities to the 'cuvette' environments of the European Old Red Sandstone.
As to the second question, your mention of the closure of the Tethyan Ocean leading to the Indian-Tibetan collision suggests that you already suspect (correctly) that the Ganges is a case in point. It's headwaters were originally in southwestern China, and it originally flowed westwards along the foot of the proto-Himalayas (what is now the high Himalayas)and out to the Indian Ocean somewhere in the vicinity of what is now the Indus basin in Pakistan. As continental collision progressed there was continental up-warping in what is now the Himachal Pradesh area of India. This reversed the Ganges drainage so that it now flows eastwards. This has important modern implications, as it was the originally westward-flowing Ganges that brought arsenic from the marine Tethyan sediments of western China, and which is now the source of the arsenic groundwater problem over much of Bangladesh and adjacent areas. See also my paper: http://link.springer.com/article/10.1007%2Fs10653-005-7102-9 But don't pay the exorbitant price! - I can send you the original text for free! :-)