A handful of eldritch weaver warp spells are assigned a different spell level for different threads. For example, true seeing is a 5th-level thread of Vision spell but a 6th-level thread of the Mind spell.
Although this isn't addressed in the Advanced Player's Manual, presumably an eldritch weaver who knows such a spell can freely choose to prepare this spell at any level at which it appears in any of his known threads. So an eldritch weaver who knows true seeing and has chosen both the thread of Vision and the thread of the Mind can prepare true seeing as either a 5th- or a 6th-level spell, as desired.
For purposes of using these multi-level spells as a prerequisite to learn additional spells, presumably the eldritch weaver must use the spell at the level it appears within the studied thread. So true seeing could be used as a prerequisite to learn a 4th- or 6th-level thread of Vision spell or a 5th- or 7th-level thread of the Mind spell, but could not be used as a prerequisite to learn a 7th-level thread of Vision spell.