The meaning of this phrase is "The sanctuary, HaShem, which your Hands have established." The vowels and trop are very instrumental in establishing this as the meaning of the phrase. The note above מקדש is a separator, essentially putting a comma between it and the following word. If it were connected to the following word, it would read "The sanctuary of HaShem which you (whoever that is) have established." If one reads the word with a מרכא note, which is an easy, lazy mistake, it might serve to connect the words and distort the meaning.
Additionally, the קמץ under the דל"ת makes the word stand alone. If it were to be mistakenly pronounced מִקְּדַשׁ, that would also imply the connection with the following word. Needless to say, both mistakes are to be avoided. I wouldn't correct the trop but I'm not so sure about the vowel.
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