It could be for several reasons. I have not checked Robertson or BDB. The structure of the two sentences are not parallel. Here are my guesses and I suppose there could be more reasons:
(1) Option 1
Perhaps a missing ἐν dropped out because the forty-six years was fronted?
[ἐν] τεσσεράκοντα καὶ ἓξ ἔτεσιν οἰκοδομήθη ὁ ναὸς οὗτος:
καὶ σὺ ἐν τρισὶν ἡμέραις ἐγερεῖς;
But note Smyth §1542
ἐν is added:
a. To words denoting time when there is no attributive: ἐν τῷ χειμῶνι in winter X. O. 17.3; cp. cross1444. b. When the attributive is a pronoun (sometimes): (ἐν) ἐκείνῃ τῇ ἡμέρᾳ. c. To statements of the time within the limits of which an event may take place (where ἐντός with the genitive is common); to statements of how much time anything takes; with numbers, ὀλίγος, πολύς, etc. Thus, ἐν τρισὶν ἡμέραις for (during) three days X. A. 4.8.8, οὐ ῥᾴδιον τὰ ἐν ἅπαντι τῷ χρόνῳ πρα_χθέντα ἐν μιᾷ ἡμέρᾳ δηλωθῆναι it is not easy to set forth in a single day the acts of all time L. 2.54, ἐξελέσθαι τὴν διαβολὴν ἐν οὕτως ὀλίγῳ χρόνῳ to clear myself of calumny in so brief a time P. A. 19a. ἐν is rarely omitted in prose, and chiefly when there is an attributive: μιᾷ νυκτὶ T. 6.27. d. Always with adjectives or adverbs used substantively: ἐν τῷ παρόντι, ἐν τῷ τότε. e. To words denoting the date of an event, not a point of time: ἐν τῇ προτέρᾳ πρεσβείᾳ in the first embassy Aes. 2.123. Thuc. employs ἐν, as ἐν τῇ ὑστεραίᾳ ἐκκλησίᾳ in the assembly held the day after 1. 44, but usu. the simple dative, as μάχῃ in the battle 3. 54, ἐκείνῃ τῇ ἐσβολῇ in that incursion 2. 20, τῇ προτέρᾳ ἐκκλησίᾳ in the first assembly 1. 44.
(2) Option 2
Or an unwritten implied participle? τεσσεράκοντα καὶ ἓξ ἔτεσιν [παραγαγουσι] οἰκοδομήθη. cf.Smyth §1498:
Dative of the Participle expressing Time.—In expressions of time a participle is often used with the dative of the person interested in the action of the subject, and especially to express the time that has passed since an action has occurred (cp. “and this is the sixth month with her, who was called barren” St. Luke i. cross36).
ἀποροῦντι δ' αὐτῷ ἔρχεται Προμηθεύς Prometheus comes to him in his perplexity P. Pr. 321c, Ξενοφῶντι πορευομένῳ οἱ ἱππεῖς ἐντυγχάνουσι πρεσβύ_ταις while Xenophon was on the march, his horsemen fell in with some old men X. A. 6.3.10. The idiom is often transferred from persons to things: ἡμέραι μάλιστα ἦσαν τῇ Μυτιλήνῃ ἑα_λωκυίᾳ ἑπτά, ὅτ' ἐς τὸ Ἔμβατον κατέπλευσαν about seven days had passed since the capture of Mytilene, when they sailed into Embatum T. 3.29. This construction is frequent in Hom. and Hdt. The participle is rarely omitted (T. 1.13.).
a. A temporal clause may take the place of the participle: τῇ στρατιᾷ, ἀφ' οὗ ἐξέπλευσεν εἰς Σικελία_ν, ἤδη ἐστὶ δύο καὶ πεντήκοντα ἔτη it is already fifty-two years since the expedition sailed to Sicily Is. 6.14.
(3) Option 3: A dative of time (past)
τεσσεράκοντα καὶ ἓξ ἔτεσιν [πάλαι] οἰκοδομήθη ὁ ναὸς οὗτος.
"forty-six years (ago) this temple was built"
The dative denotes the time at which an action takes place and the date of an event.
ταύτην μὲν τὴν ἡμέρα_ν αὐτοῦ ἔμειναν, τῇ δὲ ὑστεραίᾳ κτλ. throughout that day they waited there, but on the day following, etc. X. H. 1.1.14. So τῇ προτεραίᾳ the day before, τῇ δευτέρᾳ the second day, Ἐλαφηβολιῶνος μηνὸς ἕκτῃ (ἡμέρᾳ) φθίνοντος on the sixth of waning Elaphebolion Aes. 2.90, ἕνῃ καὶ ϝέᾳ on the last of the month D. 18.29; τρίτῳ μηνί in the third month L. 21.1, περιιόντι τῷ θέρει when summer was coming to an end T. 1.30, ἐξηκοστῷ ἔτει in the sixtieth year 1. 12; also with ὥρᾳ (χειμῶνος ὥρᾳ in the winter season And. 1.137).