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Wa alaikum assalaam wa rahmatu Allahi wa barakatuh.
1. You are referring to two different markings over some letters in the Qur'an.
The first one is called,, (the round zero) and it is found in some places over one of the three letters, alif, wow, and ya’. When any of these letters has the above symbol over it, the letter is not pronounced in any case; meaning it does not matter if we are stopping or continuing, we do not pronounce this letter.
The second marking to be noted is referred to as (the standing oblong zero). This marking is found on some alifaat that are at the end of a word, and the following word starts with a voweled letter. When we see this marking, we read the alif when stopping on this word, but eliminate the alif in pronunciation when continuing reading, joining the word with the next word, but without the alif. In addition to the examples in the question, below are some other examples:
2. There are two ways of stopping on the word in the phrase, reading Hafs 'an 'Aasim min tareeq Ash-Shatibiyyah, ; one is by reading the alif on the end with a natural lengthening of two vowel counts, the other way is by dropping the alif and stopping on the letter with a presented sukoon. The marking on the alif here then represents one of the two possible allowed ways of stopping by Hafs 'an 'Aasim min tareeq Ash-Shaatibiyyah.
May Allah reward you for your questions.
Wa assalaam alaikum wa rahmatu Allah.