I have had similar issue in my ashtanga practise at certain times eg when first learning to float to sitting, jumping back from in “position” etc.
When it flares up i stop doing full jump thrus/backs ie either walk, step back or miss a few vinyasas or easy jump throughs where my hands are on floor in front of hips etc.
[B][I][U]My personal experience shown me[/U][/I][/B] that,
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i need keep even pressure in whole hand in jump thrus
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in updog i need to focus on raising heart centre as opposed to chest and shoulders
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i can still perform whole primary series when shoulder is tender - i just modify asanas (they can be all modified to place less pressure shoulders) and transitions
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coming from a surfing and swimming background and going to ashtanga has shown that shoulder strength does not equal shoulder flexibility / mobility
Give it some rest, whether restorative poses or easy ashtanga. I practised ashtanga (jois style) for ten yrs and my shoulders are still ok and improving, just need be mindful of what your own shoulders are capable of