regex - How to concatenate multiples lines under first occurence of the header using Unix commands?

Question

I have a file like this:

Query=scaffold1_size75580
lcl|Os10t0535800-01
Query=scaffold1_size75580
lcl|Os10t0536000-02
Query=scaffold1_size75580
lcl|Os10t0536100-01
Query=scaffold1_size75580
lcl|Os10t0536400-01
Query=scaffold1_size75580
lcl|Os10t0536700-01
Query=scaffold1_size75580
lcl|Os10t0536700-01
Query=scaffold1_size75580
lcl|Os10t0536900-00
Query=scaffold1_size75580
lcl|Os10t0536700-01
Query=scaffold1_size75580
lcl|Os10t0536700-01
Query=scaffold2_size74975
lcl|Os11t0637501-00
Query=scaffold2_size74975
lcl|Os11t0637600-00
Query=scaffold2_size74975
lcl|Os11t0637800-01
Query=scaffold2_size74975
lcl|Os11t0637800-01
Query=scaffold2_size74975
lcl|Os11t0638200-00
Query=scaffold2_size74975
lcl|Os11t0638700-00
Query=scaffold2_size74975
lcl|Os11t0638700-00
Query=scaffold2_size74975
lcl|Os11t0638700-00
Query=scaffold2_size74975
lcl|Os11t0638700-00
Query=scaffold2_size74975
lcl|Os11t0638700-00
Query=scaffold2_size74975
lcl|Os11t0638900-01
Query=scaffold2_size74975
lcl|Os11t0638900-01
Query=scaffold3_size69500
lcl|Os06t0725100-01
Query=scaffold3_size69500
lcl|Os06t0724900-01
Query=scaffold3_size69500
lcl|Os06t0724900-01
Query=scaffold3_size69500
lcl|Os06t0724700-01
Query=scaffold3_size69500
lcl|Os06t0724700-01
Query=scaffold3_size69500
lcl|Os06t0724600-01
Query=scaffold3_size69500
lcl|Os06t0724100-02
Query=scaffold3_size69500
lcl|Os06t0724100-02
Query=scaffold3_size69500
lcl|Os06t0724100-02
Query=scaffold3_size69500
lcl|Os06t0724100-02
Query=scaffold4_size68019
lcl|Os01t0627550-00
Query=scaffold4_size68019
lcl|Os01t0626900-01
Query=scaffold4_size68019
lcl|Os01t0626400-01
Query=scaffold4_size68019
lcl|Os01t0626400-01
Query=scaffold4_size68019
lcl|Os01t0626400-01
Query=scaffold4_size68019
lcl|Os01t0626100-01
Query=scaffold4_size68019
lcl|Os01t0626100-01
Query=scaffold4_size68019
lcl|Os01t0626100-01
Query=scaffold4_size68019
lcl|Os01t0626032-01
Query=scaffold5_size66739
lcl|Os04t0653200-01
Query=scaffold5_size66739
lcl|Os04t0653400-01
Query=scaffold5_size66739
lcl|Os04t0653400-01
Query=scaffold5_size66739
lcl|Os04t0653600-01
Query=scaffold5_size66739
lcl|Os04t0654600-01
Query=scaffold5_size66739
lcl|Os04t0654600-01
Query=scaffold5_size66739
lcl|Os04t0654600-01
Query=scaffold5_size66739
lcl|Os04t0654600-01
Query=scaffold5_size66739
lcl|Os04t0654600-01
Query=scaffold5_size66739
lcl|Os04t0654600-01
Query=scaffold5_size66739
lcl|Os04t0654600-01
Query=scaffold5_size66739
lcl|Os04t0654600-01
Query=scaffold5_size66739
lcl|Os04t0654600-01
Query=scaffold6_size65486
lcl|Os01t0259900-00
Query=scaffold6_size65486
lcl|Os01t0259400-01
Query=scaffold6_size65486
lcl|Os01t0259400-01
Query=scaffold6_size65486
lcl|Os01t0259400-01
Query=scaffold6_size65486
lcl|Os01t0259400-01
Query=scaffold6_size65486
lcl|Os01t0259200-01
Query=scaffold7_size64123
lcl|Os04t0162100-01
Query=scaffold7_size64123
lcl|Os05t0325000-00
Query=scaffold7_size64123
lcl|Os05t0325000-00
Query=scaffold7_size64123
lcl|Os05t0325000-00
Query=scaffold7_size64123
lcl|Os05t0324600-01
Query=scaffold7_size64123
lcl|Os05t0324600-01

and so on till scaffolds in some 66000. I want my file to have duplicate headers be removed and all the corresponding entries to come within a single header, i.e., I want like this:

Query=scaffold1_75580
lcl|Os10t0535800-01
lcl|Os10t0536000-02
lcl|Os10t0536100-01
lcl|Os10t0536400-01
lcl|Os10t0536700-01
lcl|Os10t0536700-01
lcl|Os10t0536900-00
lcl|Os10t0536700-01
lcl|Os10t0536700-01
Query=scaffold2_size74975
lcl|Os11t0637501-00
lcl|Os11t0637600-00
lcl|Os11t0637800-01
lcl|Os11t0637800-01
lcl|Os11t0638200-00
lcl|Os11t0638700-00
lcl|Os11t0638700-00
lcl|Os11t0638700-00
lcl|Os11t0638700-00
lcl|Os11t0638700-00
lcl|Os11t0638900-01
lcl|Os11t0638900-01
Query=scaffold3_size69500
lcl|Os06t0725100-01
lcl|Os06t0724900-01
lcl|Os06t0724900-01
lcl|Os06t0724700-01
lcl|Os06t0724700-01
lcl|Os06t0724600-01
lcl|Os06t0724100-02
lcl|Os06t0724100-02
lcl|Os06t0724100-02
lcl|Os06t0724100-02

and so on. How to do this?

Answer 1

If you don't mind pushing this through multiple passes, I might suggest this:

Search:

^(Query=.*
)((?:(?!Query=).*
)+)1

Replace:

12

Live demo