Just a possibility, but the missing records may have to do with the 1906 Naturalization Act that went into effect September 27, 1906. I noticed the case just before Abraham's was dated September 24, 1906.
The new law brought new rules, forms, and fees, and across the country many immigrants rushed to naturalize under the old rules before the new law went into effect. Under the old rules, a petition could be filed and heard by the court the same day. The 24th was a Monday, so there were still two full days for any remaining petitions to be heard under the old law. But maybe the court did not hear all petitions filed before the time ran out?
If so, I don't think the petition would be any good after Sept 26th. I just read the naturalization regulations and law of 1906 and it goes on at length to explain that declarations filed prior to Sept. 27, 1906, were still good and would never expire. But it says nothing about petitions except to say all petitions decided by the court after the 26th had to follow the new rules.
It could be that all the missing petitions were heard and granted prior to the new law taking effect and that the new law had nothing to do with it. But, given the timing, it is also possible those petitions did not get heard/decided by the deadline and became moot. They should have remained on file but the clerk may have decided to remove them as they had no legal value. Again, just speculating.
That court's records on FamilySearch only date to late September 1906. It is possible Abraham filed a new petition in that or another court at a later date.