Vijay, you can neutralise the long chain PTSA salts by a cautious aqueous bicarbonate /DCM or ethyl acetate etc. extraction. Emulsions will form but can be dealt with. Then you can isolate the free base from the DCM and re-acidify with HCl.You can even dissolve the amino acid ester in something like THF and acidifying with HCl will probably cause the salt to precipitate nicely from the solvent.
An alternative to an aqueous bicarbonate workup is to stir the PTSA amino acid ester salt in a solvent it dissolves in and use a heterogenous base such as sodium carbonate and vigorously stir together for a few hours. You can use TLC with ninhydrin stain to determine if the amino acid is freebase or still salt.
The details from the 2 references I have (see links) dissolved the PTSA salt of the amino acid ester in Chloroform and washed with 10% sodium carbonate then dried over sodium or magnesium sulfate and concentrated the product by rotary evaporation. The crystalline HCl salt was formed with 5% concentrated aqueous HCl in Acetone in the cold, and then recrystallized from acetone.
Langmuir, 2012, 28 (25), p 9259–9266 DOI: 10.1021/la301442f
Langmuir, 2015, 31 (35), p 9546–9556 DOI: 10.1021/acs.langmuir.5b02475